NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]
DNA-(apurinic or apyrimidinic site) lyase
DNA repair enzyme that is part of the base excision repair (BER) pathway; protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates.
Contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. Contains a helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif).
Belongs to the archaeal N-glycosylase/DNA lyase (AGOG) family.
Binds double-stranded DNA tightly but without sequence specificity. It is distributed uniformly and abundantly on the chromosome, suggesting a role in chromatin architecture. However, it does not significantly compact DNA. Binds rRNA and mRNA in vivo. May play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes.
Acetylated. Deacetylation by the SIR2-homolog deacetylase may regulate its activity.
Belongs to the histone-like Alba family.
Metalloproteases ('zincins'), catalytic domain
Probable zinc metalloprotease whose natural substrate is unknown.
Binds 2 Zn(2+) ions per subunit. One is catalytic, whereas the other seems to have a structural role.
7-cyano-7-deazaguanine tRNA-ribosyltransferase
Exchanges the guanine residue with 7-cyano-7-deazaguanine (preQ0) at position 15 in the dihydrouridine loop (D-loop) of archaeal tRNAs.
Belongs to the archaeosine tRNA-ribosyltransferase family.
CRISPR-associated endonuclease Cas1, C-terminal domain
CRISPR-associated endonuclease Cas1, N-terminal domain
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette.
Homodimer, forms a heterotetramer with a Cas2 homodimer.
Belongs to the CRISPR-associated endonuclease Cas1 family.
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Functions as a ssRNA-specific endoribonuclease. Involved in the integration of spacer DNA into the CRISPR cassette.
Homodimer, forms a heterotetramer with a Cas1 homodimer.
Belongs to the CRISPR-associated endoribonuclease Cas2 protein family.
CCA tRNA nucleotidyltransferase, domain 2
Poly(A) polymerase predicted RNA binding domain
PAP/Archaeal CCA-adding enzyme, C-terminal domain
Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate.
A single active site specifically recognizes both ATP and CTP and is responsible for their addition.
Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Archaeal CCA-adding enzyme subfamily.
CRISPR-associated endodeoxyribonuclease Cas12f2
CRISPR-associated endodeoxyribonuclease Cas14b4
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids (Probable). CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA), which requires a trans-encoded small RNA (tracrRNA), but not this protein (in vitro) (By similarity). Recognizes a short motif in the CRISPR repeat sequences (the 5' PAM or protospacer adjacent motif, TTAT in this organism) to help distinguish self versus nonself, as targets within the CRISPR locus do not have PAMs (PubMed:32246713). Upon expression in E.coli of this protein, a mini CRISPR array and the probable tracrRNA, has dsDNA endonuclease activity. DNA cleavage is centered around positions 21 base pairs 3' of PAM. The mini system does not protect E.coli against transformation by foreign plasmids (PubMed:32246713).
An asymmetric homodimer. Guide RNA is probably required for dimerization.
Has an asymmetric bilobed structure, with a recognition (REC) lobe and nuclease (NUC) lobe; the sgRNA:target DNA is bound between the 2 lobes. The REC lobe (residues 1-312) is formed by the WED, ZF and REC domains, while the NUC lobe (residues 321-529) is formed by the RuvC and TNB domains. Has a split RuvC-like domain with the nuclease active sites.
Belongs to the CRISPR-associated endonuclease Cas12f family.
Bifunctional enzyme that catalyzes both the deamination of dCTP to dUTP and the hydrolysis of dUTP to dUMP without releasing the toxic dUTP intermediate.
RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. Also part of the exosome, which is a complex involved in RNA degradation. Acts as a poly(A)-binding protein that enhances the interaction between heteromeric, adenine-rich transcripts and the exosome.
Forms a ternary complex with MCM helicase and DNA. Component of the archaeal exosome complex.
Belongs to the archaeal DnaG primase family.
DNA ligase, ATP-dependent, N-terminal domain
ATP-dependent DNA ligase DNA-binding domain
DNA ligase/mRNA capping enzyme, catalytic domain
DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.
Belongs to the ATP-dependent DNA ligase family.
Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (By similarity).
Heterodimer of a large subunit and a small subunit.
Belongs to the archaeal DNA polymerase II family.
P-loop containing nucleotide triphosphate hydrolases
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
P-loop containing nucleoside triphosphate hydrolases
This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily.
Promotes the exchange of GDP for GTP in EF-1-alpha/GDP, thus allowing the regeneration of EF-1-alpha/GTP that could then be used to form the ternary complex EF-1-alpha/GTP/AAtRNA.
Belongs to the EF-1-beta/EF-1-delta family.
Elongation Factor G (Translational Gtpase), domain 3
Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome.
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily.
tRNA intron endonuclease, N-terminal domain
tRNA-intron endonuclease catalytic domain-like
tRNA-intron endonuclease N-terminal domain-like
Endonuclease that removes tRNA introns. Cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-OH termini. Recognizes a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp.
Homotetramer; although the tetramer contains four active sites, only two participate in the cleavage. Therefore, it should be considered as a dimer of dimers.
Belongs to the tRNA-intron endonuclease family. Archaeal short subfamily.
5' to 3' exonuclease, C-terminal subdomain
Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA (By similarity).
Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.
Interacts with PCNA. PCNA stimulates the nuclease activity without altering cleavage specificity.
Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily.
S-adenosyl-L-methionine-dependent methyltransferases
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.
Interacts with nop5. Component of box C/D small ribonucleoprotein (sRNP) particles that contain rpl7ae, FlpA and nop5, plus a guide RNA.
Belongs to the methyltransferase superfamily. Fibrillarin family.
Glutamyl-tRNA(Gln) amidotransferase subunit D
Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate (By similarity).
Belongs to the asparaginase 1 family. GatD subfamily.
EUKARYOTIC TRANSLATION INITIATION FACTOR
EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 2
Translation initiation factor 2 beta, aIF2beta, N-terminal domain
Zinc-binding domain of translation initiation factor 2 beta
Translation initiation factor 2 subunit beta
eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA.
Heterotrimer composed of an alpha, a beta and a gamma chain.
EUKARYOTIC TRANSLATION INITIATION FACTOR 5A
TRANSLATION INITIATION FACTOR 5A FAMILY MEMBER
Functions by promoting the formation of the first peptide bond.
EUKARYOTIC TRANSLATION INITIATION FACTOR 6
Binds to the 50S ribosomal subunit and prevents its association with the 30S ribosomal subunit to form the 70S initiation complex.
Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions.
TRNA N6-ADENOSINE THREONYLCARBAMOYLTRANSFERASE
TRNA N6-ADENOSINE THREONYLCARBAMOYLTRANSFERASE-RELATED
t(6)A37 threonylcarbamoyladenosine biosynthesis protein Kae1
tRNA threonylcarbamoyladenosine biosynthesis protein Kae1
Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37.
COMPONENT OF ATP-DEPENDENT DSDNA EXONUCLEASE
DNA double-strand break repair protein Mre11
Part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair. The complex may facilitate opening of the processed DNA ends to aid in the recruitment of HerA and NurA. Mre11 binds to DSB ends and has both double-stranded 3'-5' exonuclease activity and single-stranded endonuclease activity.
Nuclease activity is regulated by Rad50.
Homodimer. Forms a heterotetramer composed of two Mre11 subunits and two Rad50 subunits.
archaeoglobus fulgidus dsm 4304 superfamily
Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Methylated DNA-protein cysteine methyltransferase, C-terminal domain
Bifunctional methyltransferase-like/endonuclease
Probable methylated-DNA--protein-cysteine methyltransferase-like
DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA (By similarity).
In the N-terminal section; belongs to the MGMT family.
In the C-terminal section; belongs to the endonuclease V family.
Lacks the potential active site region of the MGMT family and therefore has probably lost the methyltransferase activity.
Proliferating cell nuclear antigen homolog
Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication.
Homotrimer. The subunits circularize to form a toroid; DNA passes through its center. Replication factor C (RFC) is required to load the toroid on the DNA.
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation.
The formation of the proteasomal ATPase PAN-20S proteasome complex, via the docking of the C-termini of PAN into the intersubunit pockets in the alpha-rings, triggers opening of the gate for substrate entry. Interconversion between the open-gate and close-gate conformations leads to a dynamic regulation of the 20S proteasome proteolysis activity.
The 20S proteasome core is composed of 14 alpha and 14 beta subunits that assemble into four stacked heptameric rings, resulting in a barrel-shaped structure. The two inner rings, each composed of seven catalytic beta subunits, are sandwiched by two outer rings, each composed of seven alpha subunits. The catalytic chamber with the active sites is on the inside of the barrel. Has a gated structure, the ends of the cylinder being occluded by the N-termini of the alpha-subunits. Is capped at one or both ends by the proteasome regulatory ATPase, PAN.
Removed in mature form; by autocatalysis
PEPTIDYL-TRNA HYDROLASE 2, MITOCHONDRIAL
The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.
DNA double-strand break repair Rad50 ATPase
Part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair. The complex may facilitate opening of the processed DNA ends to aid in the recruitment of HerA and NurA. Rad50 controls the balance between DNA end bridging and DNA resection via ATP-dependent structural rearrangements of the Rad50/Mre11 complex.
The two conserved Cys that bind zinc constitute the zinc-hook, which separates the large intramolecular coiled coil regions. The 2 Cys residues coordinate one molecule of zinc with the help of the 2 Cys residues of the zinc-hook of another Rad50 molecule, thereby forming a V-shaped homodimer.
Belongs to the SMC family. RAD50 subfamily.
MEIOTIC RECOMBINATION PROTEIN DMC1/LIM15 HOMOLOG
RECA/RAD51/RADA DNA STRAND-PAIRING FAMILY MEMBER
DNA repair and recombination protein RadA
Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules.
Belongs to the eukaryotic RecA-like protein family.
CHROMOSOME TRANSMISSION FIDELITY FACTOR 18
Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.
Heteromultimer composed of small subunits (RfcS) and large subunits (RfcL).
Belongs to the activator 1 small subunits family. RfcL subfamily.
REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT
Belongs to the activator 1 small subunits family. RfcS subfamily.
Belongs to the universal ribosomal protein uL16 family.
Ribosomal protein L11, C-terminal domain
Ribosomal protein L11/L12, N-terminal domain
39S RIBOSOMAL PROTEIN L11, MITOCHONDRIAL
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.
Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex.
Belongs to the universal ribosomal protein uL11 family.
This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.
Belongs to the universal ribosomal protein uL13 family.
Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.
Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Belongs to the universal ribosomal protein uL14 family.
Belongs to the eukaryotic ribosomal protein eL15 family.
Part of the 50S ribosomal subunit. Binds 23S rRNA.
Belongs to the eukaryotic ribosomal protein eL20 family.
Belongs to the eukaryotic ribosomal protein eL18 family.
This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.
Part of the 50S ribosomal subunit. Contacts the 5S and 23S rRNAs.
Belongs to the universal ribosomal protein uL18 family.
Binds directly to 23S rRNA. Probably involved in E site tRNA release.
Protein L1 is also a translational repressor protein, it controls the translation of its operon by binding to its mRNA.
Belongs to the universal ribosomal protein uL1 family.
Belongs to the eukaryotic ribosomal protein eL21 family.
This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.
The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome.
Belongs to the universal ribosomal protein uL22 family.
RIBOSOMAL_L23EN DOMAIN-CONTAINING PROTEIN
Binds to 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome.
Part of the 50S ribosomal subunit. Contacts protein L29.
Belongs to the universal ribosomal protein uL23 family.
One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
Located at the polypeptide exit tunnel on the outside of the subunit.
Belongs to the universal ribosomal protein uL24 family.
Belongs to the universal ribosomal protein uL29 family.
One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.
Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome.
Belongs to the universal ribosomal protein uL2 family.
Ribosomal protein L30, ferredoxin-like fold domain
Belongs to the universal ribosomal protein uL30 family.
60S RIBOSOMAL PROTEIN L32 AND DNA-DIRECTED RNA POLYMERASE II, SUBUNIT N
Belongs to the eukaryotic ribosomal protein eL32 family.
Belongs to the eukaryotic ribosomal protein eL43 family. Putative zinc-binding subfamily.
One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L24e.
Belongs to the universal ribosomal protein uL3 family.
One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.
Forms part of the polypeptide exit tunnel.
Belongs to the universal ribosomal protein uL4 family.
This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. May contact the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.
Part of the 50S ribosomal subunit; contacts the 5S rRNA and probably tRNA. Forms a bridge to the 30S subunit in the 70S ribosome.
Belongs to the universal ribosomal protein uL5 family.
This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.
Belongs to the universal ribosomal protein uL6 family.
Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs.
Part of the 50S ribosomal subunit. Probably part of the RNase P complex.
Belongs to the eukaryotic ribosomal protein eL8 family.
Ribonuclease H-like superfamily/Ribonuclease H
Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding.
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 FAMILY MEMBER
DNA-directed RNA polymerase subunit Rpo10
DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
Belongs to the archaeal Rpo10/eukaryotic RPB10 RNA polymerase subunit family.
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
DNA-directed RNA polymerase subunit Rpo11
Belongs to the archaeal Rpo11/eukaryotic RPB11/RPC19 RNA polymerase subunit family.
Involved in the binding of tRNA to the ribosomes.
Belongs to the universal ribosomal protein uS10 family.
40S RIBOSOMAL PROTEIN S14/30S RIBOSOMAL PROTEIN S11
Located on the platform of the 30S subunit.
Belongs to the universal ribosomal protein uS11 family.
With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits.
Belongs to the universal ribosomal protein uS12 family.
30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18
Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement.
Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome.
Belongs to the universal ribosomal protein uS13 family.
Glucocorticoid receptor-like (DNA-binding domain)
Binds 16S rRNA, required for the assembly of 30S particles.
Belongs to the universal ribosomal protein uS14 family. Zinc-binding uS14 subfamily.
Belongs to the universal ribosomal protein uS15 family.
Belongs to the eukaryotic ribosomal protein eS17 family.
One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.
Belongs to the universal ribosomal protein uS17 family.
Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.
Belongs to the universal ribosomal protein uS19 family.
Belongs to the eukaryotic ribosomal protein eS24 family.
Belongs to the eukaryotic ribosomal protein eS31 family.
Belongs to the eukaryotic ribosomal protein eS28 family.
Belongs to the universal ribosomal protein uS2 family.
Belongs to the eukaryotic ribosomal protein eS1 family.
Prokaryotic type KH domain (KH-domain type II)
Binds the lower part of the 30S subunit head.
Belongs to the universal ribosomal protein uS3 family.
Belongs to the eukaryotic ribosomal protein eS4 family.
One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.
With S5 and S12 plays an important role in translational accuracy.
Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity.
Belongs to the universal ribosomal protein uS4 family.
With S4 and S12 plays an important role in translational accuracy.
Part of the 30S ribosomal subunit. Contacts protein S4.
The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity.
Belongs to the universal ribosomal protein uS5 family.
Belongs to the eukaryotic ribosomal protein eS6 family.
One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center.
Belongs to the universal ribosomal protein uS7 family.
Belongs to the eukaryotic ribosomal protein eS8 family.
One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit.
Belongs to the universal ribosomal protein uS8 family.
3'-phosphate/5'-hydroxy nucleic acid ligase
Essential for tRNA splicing and maturation. Acts by directly joining spliced tRNA halves to mature-sized tRNAs. Joins RNA with 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy ends.
Ligation proceeds through 3 nucleotidyl transfer steps, with 2',3'-cyclic phosphate termini being hydrolyzed to 3'-P termini in a step that precedes 3'-P activation with GMP. In the first nucleotidyl transfer step, RtcB reacts with GTP to form a covalent RtcB-histidine-GMP intermediate with release of PPi; in the second step, the GMP moiety is transferred to the RNA 3'-P; in the third step, the 5'-OH from the opposite RNA strand attacks the activated 3'-P to form a 3',5'-phosphodiester bond and release GMP.
Cysteine-tRNA ligase, C-terminal anti-codon recognition domain
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Belongs to the class-I aminoacyl-tRNA synthetase family.
Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).
Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 2 subfamily.
Belongs to the class-II aminoacyl-tRNA synthetase family.
Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
Methionyl-tRNA synthetase (MetRS), Zn-domain
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.
Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 1 subfamily.
BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro).
Consists of three domains: the N-terminal catalytic domain, the anticodon-binding domain and the C-terminal extension.
Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily.
THREONINE--TRNA LIGASE, CHLOROPLASTIC/MITOCHONDRIAL 2
Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr).
The N-terminal domain is an archaea-specific tRNA-editing domain that hydrolyzes incorrectly charged L-seryl-tRNA(Thr). Catalysis of tRNA editing is performed by the charged tRNA itself.
VALINE--TRNA LIGASE, CHLOROPLASTIC/MITOCHONDRIAL 2
Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner (By similarity).
ValRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated threonine is translocated from the active site to the editing site (By similarity).
Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 2 subfamily.
Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).
Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 4 subfamily.
tRNA (guanine(37)-N1)/4-demethylwyosine(37)-methyltransferase Taw22
Catalyzes both the N1-methylation of guanosine and the C7-methylation of 4-demethylwyosine (imG-14) at position 37 in tRNA(Phe).
Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM5/TYW2 family.
Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides.
Homodecamer. Pentamer of dimers that assemble into a ring structure.
The active site is a conserved redox-active cysteine residue, the peroxidatic cysteine (C(P)), which makes the nucleophilic attack on the peroxide substrate. The peroxide oxidizes the C(P)-SH to cysteine sulfenic acid (C(P)-SOH), which then reacts with another cysteine residue, the resolving cysteine (C(R)), to form a disulfide bridge. The disulfide is subsequently reduced by an appropriate electron donor to complete the catalytic cycle. Although the primary sequence of this enzyme is similar to those of the 1-Cys Prx6 enzymes, its catalytic properties resemble those of the typical 2-Cys Prxs and C(R) is provided by the other dimeric subunit to form an intersubunit disulfide. The disulfide is subsequently reduced by thioredoxin.
Belongs to the peroxiredoxin family. Prx6 subfamily.
Cysteine sulfenic acid (-SOH) intermediate
Transcription factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Facilitates transcription initiation by enhancing TATA-box recognition by TATA-box-binding protein (Tbp), and transcription factor B (Tfb) and RNA polymerase recruitment. Not absolutely required for transcription in vitro, but particularly important in cases where Tbp or Tfb function is not optimal. It dynamically alters the nucleic acid-binding properties of RNA polymerases by stabilizing the initiation complex and destabilizing elongation complexes. Seems to translocate with the RNA polymerase following initiation and acts by binding to the non template strand of the transcription bubble in elongation complexes.
Monomer. Interaction with RNA polymerase subunits RpoF and RpoE is necessary for Tfe stimulatory transcription activity. Able to interact with Tbp and RNA polymerase in the absence of DNA promoter. Interacts both with the preinitiation and elongation complexes.
The winged helix domain is involved in binding to DNA in the preinitiation complex.
Pseudouridine synthase I, catalytic domain, C-terminal subdomain
Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.
Belongs to the tRNA pseudouridine synthase TruA family.
CENTROMERE/MICROTUBULE BINDING PROTEIN CBF5
H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT DKC1
Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.
Belongs to the pseudouridine synthase TruB family. Type 2 subfamily.
Could be responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs.
Belongs to the pseudouridine synthase TruD family.
V-TYPE PROTON ATPASE CATALYTIC SUBUNIT A
C-terminal domain of alpha and beta subunits of F1 ATP synthase
N-terminal domain of alpha and beta subunits of F1 ATP synthase
Produces ATP from ADP in the presence of a proton gradient across the membrane. The archaeal alpha chain is a catalytic subunit.
Belongs to the ATPase alpha/beta chains family.
TRNA (URACIL(54)-C(5))-METHYLTRANSFERASE
Uncharacterized RNA methyltransferase NEQ053
Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.
UPF0173 METAL-DEPENDENT HYDROLASE MJ1163-RELATED
UPF0173 METAL-DEPENDENT HYDROLASE TM_1162
UPF0173 metal-dependent hydrolase NEQ378