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Protein

tRNA U34 carboxymethyltransferase

Gene

cmoB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes carboxymethyl transfer from carboxy-S-adenosyl-L-methionine (Cx-SAM) to 5-hydroxyuridine (ho5U) to form 5-carboxymethoxyuridine (cmo5U) at position 34 in tRNAs. Can also catalyze the SAM-dependent methylation of ho5U, with much lower efficiency.2 Publications

Catalytic activityi

5-hydroxyuridine(34) in tRNA + carboxy-S-adenosyl-L-methionine = 5-carboxymethoxyuridine(34) in tRNA + S-adenosyl-L-homocysteine.UniRule annotation2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei91 – 911Carboxy-S-adenosyl-L-methionineUniRule annotationCombined sources
Binding sitei105 – 1051Carboxy-S-adenosyl-L-methionineUniRule annotationCombined sources
Binding sitei110 – 1101Carboxy-S-adenosyl-L-methionineUniRule annotationCombined sources
Binding sitei130 – 1301Carboxy-S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotationCombined sources
Binding sitei196 – 1961Carboxy-S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotationCombined sources
Binding sitei200 – 2001Carboxy-S-adenosyl-L-methionineUniRule annotationCombined sources
Binding sitei315 – 3151Carboxy-S-adenosyl-L-methionineUniRule annotationCombined sources

GO - Molecular functioni

GO - Biological processi

  • methylation Source: GO_Central
  • protein homotetramerization Source: EcoCyc
  • tRNA wobble uridine modification Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

tRNA processing

Enzyme and pathway databases

BioCyciEcoCyc:G7021-MONOMER.
ECOL316407:JW1860-MONOMER.
MetaCyc:G7021-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA U34 carboxymethyltransferaseUniRule annotationCurated (EC:2.5.1.-UniRule annotation2 Publications)
Gene namesi
Name:cmoB1 PublicationUniRule annotation
Synonyms:yecP
Ordered Locus Names:b1871, JW1860
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14034. cmoB.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi91 – 911K → A: Decreases affinity toward Cx-SAM and increases affinity toward SAM. Lack of carboxymethyltransferase activity, but can still produce mho5U.
Mutagenesisi200 – 2001Y → A: Slight decrease in Cx-SAM binding affinity. Does not affect carboxymethyltransferase activity.
Mutagenesisi315 – 3151R → A: Slight decrease in Cx-SAM binding affinity. Does not affect carboxymethyltransferase activity.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 323323tRNA U34 carboxymethyltransferasePRO_0000169085Add
BLAST

Proteomic databases

PaxDbiP76291.
PRIDEiP76291.

Interactioni

Subunit structurei

Homotetramer.UniRule annotation1 Publication

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4260349. 8 interactions.
IntActiP76291. 7 interactions.
STRINGi511145.b1871.

Structurei

Secondary structure

1
323
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 117Combined sources
Helixi17 – 215Combined sources
Helixi23 – 3311Combined sources
Helixi38 – 4811Combined sources
Beta strandi55 – 628Combined sources
Beta strandi64 – 663Combined sources
Helixi73 – 8412Combined sources
Beta strandi94 – 963Combined sources
Beta strandi99 – 1013Combined sources
Beta strandi104 – 1063Combined sources
Helixi107 – 1148Combined sources
Helixi115 – 1173Combined sources
Beta strandi125 – 1295Combined sources
Helixi135 – 1428Combined sources
Beta strandi146 – 1516Combined sources
Helixi155 – 16713Combined sources
Beta strandi173 – 1775Combined sources
Helixi181 – 1833Combined sources
Beta strandi190 – 1978Combined sources
Helixi199 – 2013Combined sources
Helixi205 – 2139Combined sources
Beta strandi216 – 22712Combined sources
Beta strandi252 – 2543Combined sources
Helixi255 – 26410Combined sources
Beta strandi268 – 27710Combined sources
Turni280 – 2823Combined sources
Helixi294 – 2974Combined sources
Beta strandi302 – 3065Combined sources
Beta strandi309 – 3113Combined sources
Beta strandi314 – 3218Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4QNUX-ray2.60A/B/C/D/E/F/G/H1-323[»]
4QNVX-ray2.64A/B1-323[»]
4QNXX-ray2.62A/B1-323[»]
ProteinModelPortaliP76291.
SMRiP76291. Positions 1-323.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni152 – 1543Carboxy-S-adenosyl-L-methionine bindingUniRule annotationCombined sources
Regioni181 – 1822Carboxy-S-adenosyl-L-methionine bindingUniRule annotationCombined sources

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. CmoB family.UniRule annotationCurated

Phylogenomic databases

eggNOGiENOG4105PFA. Bacteria.
COG0500. LUCA.
HOGENOMiHOG000218456.
InParanoidiP76291.
KOiK15257.
OMAiCEWRSDF.
OrthoDBiEOG6PZX8S.
PhylomeDBiP76291.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01590. tRNA_carboxymethyltr_CmoB.
InterProiIPR010017. CmoB.
IPR027555. mo5U34_MeTrfas-like.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF08003. Methyltransf_9. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00452. TIGR00452. 1 hit.

Sequencei

Sequence statusi: Complete.

P76291-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIDFGNFYSL IAKNHLSHWL ETLPAQIANW QREQQHGLFK QWSNAVEFLP
60 70 80 90 100
EIKPYRLDLL HSVTAESEEP LSAGQIKRIE TLMRNLMPWR KGPFSLYGVN
110 120 130 140 150
IDTEWRSDWK WDRVLPHLSD LTGRTILDVG CGSGYHMWRM IGAGAHLAVG
160 170 180 190 200
IDPTQLFLCQ FEAVRKLLGN DQRAHLLPLG IEQLPALKAF DTVFSMGVLY
210 220 230 240 250
HRRSPLEHLW QLKDQLVNEG ELVLETLVID GDENTVLVPG DRYAQMRNVY
260 270 280 290 300
FIPSALALKN WLKKCGFVDI RIADVSVTTT EEQRRTEWMV TESLADFLDP
310 320
HDPGKTVEGY PAPKRAVLIA RKP
Length:323
Mass (Da):37,007
Last modified:February 1, 1997 - v1
Checksum:i2954B076A83607A3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74941.1.
AP009048 Genomic DNA. Translation: BAA15681.1.
PIRiG64949.
RefSeqiNP_416385.1. NC_000913.3.
WP_000564725.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74941; AAC74941; b1871.
BAA15681; BAA15681; BAA15681.
GeneIDi946387.
KEGGiecj:JW1860.
eco:b1871.
PATRICi32119065. VBIEscCol129921_1950.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74941.1.
AP009048 Genomic DNA. Translation: BAA15681.1.
PIRiG64949.
RefSeqiNP_416385.1. NC_000913.3.
WP_000564725.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4QNUX-ray2.60A/B/C/D/E/F/G/H1-323[»]
4QNVX-ray2.64A/B1-323[»]
4QNXX-ray2.62A/B1-323[»]
ProteinModelPortaliP76291.
SMRiP76291. Positions 1-323.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260349. 8 interactions.
IntActiP76291. 7 interactions.
STRINGi511145.b1871.

Proteomic databases

PaxDbiP76291.
PRIDEiP76291.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74941; AAC74941; b1871.
BAA15681; BAA15681; BAA15681.
GeneIDi946387.
KEGGiecj:JW1860.
eco:b1871.
PATRICi32119065. VBIEscCol129921_1950.

Organism-specific databases

EchoBASEiEB3788.
EcoGeneiEG14034. cmoB.

Phylogenomic databases

eggNOGiENOG4105PFA. Bacteria.
COG0500. LUCA.
HOGENOMiHOG000218456.
InParanoidiP76291.
KOiK15257.
OMAiCEWRSDF.
OrthoDBiEOG6PZX8S.
PhylomeDBiP76291.

Enzyme and pathway databases

BioCyciEcoCyc:G7021-MONOMER.
ECOL316407:JW1860-MONOMER.
MetaCyc:G7021-MONOMER.

Miscellaneous databases

PROiP76291.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01590. tRNA_carboxymethyltr_CmoB.
InterProiIPR010017. CmoB.
IPR027555. mo5U34_MeTrfas-like.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF08003. Methyltransf_9. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00452. TIGR00452. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function."
    Kim J., Xiao H., Bonanno J.B., Kalyanaraman C., Brown S., Tang X., Al-Obaidi N.F., Patskovsky Y., Babbitt P.C., Jacobson M.P., Lee Y.S., Almo S.C.
    Nature 498:123-126(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  5. "Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification."
    Kim J., Xiao H., Koh J., Wang Y., Bonanno J.B., Thomas K., Babbitt P.C., Brown S., Lee Y.S., Almo S.C.
    Nucleic Acids Res. 43:4602-4613(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH CARBOXY-S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF LYS-91; TYR-200 AND ARG-315.

Entry informationi

Entry nameiCMOB_ECOLI
AccessioniPrimary (citable) accession number: P76291
Secondary accession number(s): O07983
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: February 1, 1997
Last modified: July 6, 2016
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.