CMOB_ECOLI
ID CMOB_ECOLI Reviewed; 323 AA.
AC P76291; O07983;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=tRNA U34 carboxymethyltransferase {ECO:0000255|HAMAP-Rule:MF_01590, ECO:0000305};
DE EC=2.5.1.- {ECO:0000255|HAMAP-Rule:MF_01590, ECO:0000269|PubMed:23676670, ECO:0000269|PubMed:25855808};
GN Name=cmoB {ECO:0000255|HAMAP-Rule:MF_01590, ECO:0000303|PubMed:23676670};
GN Synonyms=yecP; OrderedLocusNames=b1871, JW1860;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA Horiuchi T.;
RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 40.1-50.0 min region on the linkage map.";
RL DNA Res. 3:379-392(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=23676670; DOI=10.1038/nature12180;
RA Kim J., Xiao H., Bonanno J.B., Kalyanaraman C., Brown S., Tang X.,
RA Al-Obaidi N.F., Patskovsky Y., Babbitt P.C., Jacobson M.P., Lee Y.S.,
RA Almo S.C.;
RT "Structure-guided discovery of the metabolite carboxy-SAM that modulates
RT tRNA function.";
RL Nature 498:123-126(2013).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH
RP CARBOXY-S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, AND
RP MUTAGENESIS OF LYS-91; TYR-200 AND ARG-315.
RX PubMed=25855808; DOI=10.1093/nar/gkv206;
RA Kim J., Xiao H., Koh J., Wang Y., Bonanno J.B., Thomas K., Babbitt P.C.,
RA Brown S., Lee Y.S., Almo S.C.;
RT "Determinants of the CmoB carboxymethyl transferase utilized for selective
RT tRNA wobble modification.";
RL Nucleic Acids Res. 43:4602-4613(2015).
CC -!- FUNCTION: Catalyzes carboxymethyl transfer from carboxy-S-adenosyl-L-
CC methionine (Cx-SAM) to 5-hydroxyuridine (ho5U) to form 5-
CC carboxymethoxyuridine (cmo5U) at position 34 in tRNAs. Can also
CC catalyze the SAM-dependent methylation of ho5U, with much lower
CC efficiency. {ECO:0000269|PubMed:23676670, ECO:0000269|PubMed:25855808}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-hydroxyuridine(34) in tRNA + carboxy-S-adenosyl-L-methionine
CC = 5-carboxymethoxyuridine(34) in tRNA + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:52848, Rhea:RHEA-COMP:13381, Rhea:RHEA-
CC COMP:13383, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:134278,
CC ChEBI:CHEBI:136877, ChEBI:CHEBI:136879; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01590, ECO:0000269|PubMed:23676670,
CC ECO:0000269|PubMed:25855808};
CC -!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_01590,
CC ECO:0000269|PubMed:25855808}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. CmoB family. {ECO:0000255|HAMAP-Rule:MF_01590,
CC ECO:0000305}.
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DR EMBL; U00096; AAC74941.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15681.1; -; Genomic_DNA.
DR PIR; G64949; G64949.
DR RefSeq; NP_416385.1; NC_000913.3.
DR RefSeq; WP_000564725.1; NZ_SSZK01000001.1.
DR PDB; 4QNU; X-ray; 2.60 A; A/B/C/D/E/F/G/H=1-323.
DR PDB; 4QNV; X-ray; 2.64 A; A/B=1-323.
DR PDB; 4QNX; X-ray; 2.62 A; A/B=1-323.
DR PDBsum; 4QNU; -.
DR PDBsum; 4QNV; -.
DR PDBsum; 4QNX; -.
DR AlphaFoldDB; P76291; -.
DR SMR; P76291; -.
DR BioGRID; 4260349; 43.
DR IntAct; P76291; 7.
DR STRING; 511145.b1871; -.
DR jPOST; P76291; -.
DR PaxDb; P76291; -.
DR PRIDE; P76291; -.
DR EnsemblBacteria; AAC74941; AAC74941; b1871.
DR EnsemblBacteria; BAA15681; BAA15681; BAA15681.
DR GeneID; 58462338; -.
DR GeneID; 946387; -.
DR KEGG; ecj:JW1860; -.
DR KEGG; eco:b1871; -.
DR PATRIC; fig|1411691.4.peg.377; -.
DR EchoBASE; EB3788; -.
DR eggNOG; COG0500; Bacteria.
DR HOGENOM; CLU_052665_0_0_6; -.
DR InParanoid; P76291; -.
DR OMA; CEWRSDF; -.
DR PhylomeDB; P76291; -.
DR BioCyc; EcoCyc:G7021-MON; -.
DR BioCyc; MetaCyc:G7021-MON; -.
DR PRO; PR:P76291; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0008168; F:methyltransferase activity; IBA:GO_Central.
DR GO; GO:0016765; F:transferase activity, transferring alkyl or aryl (other than methyl) groups; IDA:EcoCyc.
DR GO; GO:0097697; F:tRNA 5-carboxymethoxyuridine methyltransferase activity; IBA:GO_Central.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IDA:EcoCyc.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_01590; tRNA_carboxymethyltr_CmoB; 1.
DR InterPro; IPR010017; CmoB.
DR InterPro; IPR027555; Mo5U34_MeTrfas-like.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF08003; Methyltransf_9; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00452; TIGR00452; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Reference proteome; Transferase; tRNA processing.
FT CHAIN 1..323
FT /note="tRNA U34 carboxymethyltransferase"
FT /id="PRO_0000169085"
FT BINDING 91
FT /ligand="carboxy-S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:134278"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01590,
FT ECO:0007744|PDB:4QNU, ECO:0007744|PDB:4QNV"
FT BINDING 105
FT /ligand="carboxy-S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:134278"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01590,
FT ECO:0007744|PDB:4QNU"
FT BINDING 110
FT /ligand="carboxy-S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:134278"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01590,
FT ECO:0007744|PDB:4QNU, ECO:0007744|PDB:4QNV"
FT BINDING 130
FT /ligand="carboxy-S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:134278"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01590,
FT ECO:0007744|PDB:4QNU, ECO:0007744|PDB:4QNV"
FT BINDING 152..154
FT /ligand="carboxy-S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:134278"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01590,
FT ECO:0007744|PDB:4QNU, ECO:0007744|PDB:4QNV"
FT BINDING 181..182
FT /ligand="carboxy-S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:134278"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01590,
FT ECO:0007744|PDB:4QNU, ECO:0007744|PDB:4QNV"
FT BINDING 196
FT /ligand="carboxy-S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:134278"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01590,
FT ECO:0007744|PDB:4QNU, ECO:0007744|PDB:4QNV"
FT BINDING 200
FT /ligand="carboxy-S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:134278"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01590,
FT ECO:0007744|PDB:4QNU, ECO:0007744|PDB:4QNV"
FT BINDING 315
FT /ligand="carboxy-S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:134278"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01590,
FT ECO:0007744|PDB:4QNU, ECO:0007744|PDB:4QNV"
FT MUTAGEN 91
FT /note="K->A: Decreases affinity toward Cx-SAM and increases
FT affinity toward SAM. Lack of carboxymethyltransferase
FT activity, but can still produce mho5U."
FT MUTAGEN 200
FT /note="Y->A: Slight decrease in Cx-SAM binding affinity.
FT Does not affect carboxymethyltransferase activity."
FT MUTAGEN 315
FT /note="R->A: Slight decrease in Cx-SAM binding affinity.
FT Does not affect carboxymethyltransferase activity."
FT HELIX 5..11
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 17..21
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 23..33
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 38..48
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 55..62
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 64..66
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 73..84
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 99..101
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 104..106
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 107..114
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 125..129
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 135..142
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 146..151
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 155..167
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 173..177
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 181..183
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 190..197
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 199..201
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 205..213
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 216..227
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 255..264
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 268..277
FT /evidence="ECO:0007829|PDB:4QNX"
FT TURN 280..282
FT /evidence="ECO:0007829|PDB:4QNX"
FT HELIX 294..297
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 302..306
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 309..311
FT /evidence="ECO:0007829|PDB:4QNX"
FT STRAND 314..321
FT /evidence="ECO:0007829|PDB:4QNX"
SQ SEQUENCE 323 AA; 37007 MW; 2954B076A83607A3 CRC64;
MIDFGNFYSL IAKNHLSHWL ETLPAQIANW QREQQHGLFK QWSNAVEFLP EIKPYRLDLL
HSVTAESEEP LSAGQIKRIE TLMRNLMPWR KGPFSLYGVN IDTEWRSDWK WDRVLPHLSD
LTGRTILDVG CGSGYHMWRM IGAGAHLAVG IDPTQLFLCQ FEAVRKLLGN DQRAHLLPLG
IEQLPALKAF DTVFSMGVLY HRRSPLEHLW QLKDQLVNEG ELVLETLVID GDENTVLVPG
DRYAQMRNVY FIPSALALKN WLKKCGFVDI RIADVSVTTT EEQRRTEWMV TESLADFLDP
HDPGKTVEGY PAPKRAVLIA RKP
