AMID_ECOLI
ID AMID_ECOLI Reviewed; 276 AA.
AC P75820;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=N-acetylmuramoyl-L-alanine amidase AmiD;
DE EC=3.5.1.28;
DE Flags: Precursor;
GN Name=amiD; Synonyms=ybjR; OrderedLocusNames=b0867, JW0851;
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=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(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 X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 18-276 IN COMPLEX WITH ZINC AND
RP N-ACETYLMURAMOYL-TRIPEPTIDE, COFACTOR, AND ACTIVE SITE.
RX PubMed=20036252; DOI=10.1016/j.jmb.2009.12.038;
RA Kerff F., Petrella S., Mercier F., Sauvage E., Herman R., Pennartz A.,
RA Zervosen A., Luxen A., Frere J.M., Joris B., Charlier P.;
RT "Specific structural features of the N-acetylmuramoyl-L-alanine amidase
RT AmiD from Escherichia coli and mechanistic implications for enzymes of this
RT family.";
RL J. Mol. Biol. 397:249-259(2010).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolyzes the link between N-acetylmuramoyl residues and L-
CC amino acid residues in certain cell-wall glycopeptides.; EC=3.5.1.28;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:20036252};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:20036252};
CC -!- SUBCELLULAR LOCATION: Cell outer membrane {ECO:0000305}; Lipid-anchor
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the N-acetylmuramoyl-L-alanine amidase 2 family.
CC {ECO:0000305}.
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DR EMBL; U00096; AAC73954.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35581.1; -; Genomic_DNA.
DR PIR; C64825; C64825.
DR RefSeq; NP_415388.1; NC_000913.3.
DR RefSeq; WP_001252135.1; NZ_SSZK01000002.1.
DR PDB; 2BH7; X-ray; 2.20 A; A=18-276.
DR PDB; 2WKX; X-ray; 1.80 A; A=18-276.
DR PDB; 3D2Y; X-ray; 1.75 A; A=18-276.
DR PDB; 3D2Z; X-ray; 2.80 A; A=18-276.
DR PDBsum; 2BH7; -.
DR PDBsum; 2WKX; -.
DR PDBsum; 3D2Y; -.
DR PDBsum; 3D2Z; -.
DR AlphaFoldDB; P75820; -.
DR SMR; P75820; -.
DR BioGRID; 4259998; 12.
DR STRING; 511145.b0867; -.
DR jPOST; P75820; -.
DR PaxDb; P75820; -.
DR PRIDE; P75820; -.
DR EnsemblBacteria; AAC73954; AAC73954; b0867.
DR EnsemblBacteria; BAA35581; BAA35581; BAA35581.
DR GeneID; 945494; -.
DR KEGG; ecj:JW0851; -.
DR KEGG; eco:b0867; -.
DR PATRIC; fig|1411691.4.peg.1410; -.
DR EchoBASE; EB3451; -.
DR eggNOG; COG3023; Bacteria.
DR HOGENOM; CLU_049290_2_1_6; -.
DR InParanoid; P75820; -.
DR OMA; DTRHPAQ; -.
DR PhylomeDB; P75820; -.
DR BioCyc; EcoCyc:G6452-MON; -.
DR BioCyc; MetaCyc:G6452-MON; -.
DR BRENDA; 3.5.1.28; 2026.
DR EvolutionaryTrace; P75820; -.
DR PRO; PR:P75820; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0009279; C:cell outer membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0019867; C:outer membrane; IDA:EcoliWiki.
DR GO; GO:0009392; F:N-acetyl-anhydromuramoyl-L-alanine amidase activity; IDA:EcoCyc.
DR GO; GO:0008745; F:N-acetylmuramoyl-L-alanine amidase activity; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoliWiki.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009253; P:peptidoglycan catabolic process; IDA:EcoCyc.
DR GO; GO:0009254; P:peptidoglycan turnover; IBA:GO_Central.
DR CDD; cd06583; PGRP; 1.
DR Gene3D; 1.10.101.10; -; 1.
DR Gene3D; 3.40.80.10; -; 1.
DR InterPro; IPR036505; Amidase/PGRP_sf.
DR InterPro; IPR002502; Amidase_domain.
DR InterPro; IPR036365; PGBD-like_sf.
DR InterPro; IPR036366; PGBDSf.
DR Pfam; PF01510; Amidase_2; 1.
DR SMART; SM00644; Ami_2; 1.
DR SUPFAM; SSF47090; SSF47090; 1.
DR SUPFAM; SSF55846; SSF55846; 1.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell outer membrane; Cell wall biogenesis/degradation;
KW Hydrolase; Lipoprotein; Membrane; Metal-binding; Palmitate;
KW Reference proteome; Signal; Zinc.
FT SIGNAL 1..16
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT CHAIN 17..276
FT /note="N-acetylmuramoyl-L-alanine amidase AmiD"
FT /id="PRO_0000164417"
FT DOMAIN 42..179
FT /note="N-acetylmuramoyl-L-alanine amidase"
FT /evidence="ECO:0000255"
FT ACT_SITE 119
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:20036252"
FT BINDING 50
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:20036252"
FT BINDING 51..52
FT /ligand="substrate"
FT BINDING 166
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:20036252"
FT BINDING 176
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:20036252"
FT SITE 174
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000269|PubMed:20036252"
FT LIPID 17
FT /note="N-palmitoyl cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT LIPID 17
FT /note="S-diacylglycerol cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT STRAND 23..25
FT /evidence="ECO:0007829|PDB:3D2Y"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:3D2Y"
FT STRAND 46..51
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 56..63
FT /evidence="ECO:0007829|PDB:3D2Y"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:3D2Y"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 111..114
FT /evidence="ECO:0007829|PDB:3D2Y"
FT STRAND 115..120
FT /evidence="ECO:0007829|PDB:3D2Y"
FT STRAND 125..128
FT /evidence="ECO:0007829|PDB:3D2Y"
FT STRAND 131..134
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 139..156
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:3D2Y"
FT STRAND 163..165
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 166..169
FT /evidence="ECO:0007829|PDB:3D2Y"
FT TURN 171..173
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 183..188
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 197..204
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 215..225
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 235..249
FT /evidence="ECO:0007829|PDB:3D2Y"
FT HELIX 260..273
FT /evidence="ECO:0007829|PDB:3D2Y"
SQ SEQUENCE 276 AA; 31072 MW; E6E4F642AFF548CD CRC64;
MRRFFWLVAA ALLLAGCAGE KGIVEKEGYQ LDTRRQAQAA YPRIKVLVIH YTADDFDSSL
ATLTDKQVSS HYLVPAVPPR YNGKPRIWQL VPEQELAWHA GISAWRGATR LNDTSIGIEL
ENRGWQKSAG VKYFAPFEPA QIQALIPLAK DIIARYHIKP ENVVAHADIA PQRKDDPGPL
FPWQQLAQQG IGAWPDAQRV NFYLAGRAPH TPVDTASLLE LLARYGYDVK PDMTPREQRR
VIMAFQMHFR PTLYNGEADA ETQAIAEALL EKYGQD
