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N-acetylmuramoyl-L-alanine amidase AmiD (EC 3.5.1.28)

 AMID_ECOLI              Reviewed;         276 AA.
P75820;
01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
01-FEB-1997, sequence version 1.
12-SEP-2018, entry version 135.
RecName: Full=N-acetylmuramoyl-L-alanine amidase AmiD;
EC=3.5.1.28;
Flags: Precursor;
Name=amiD; Synonyms=ybjR; OrderedLocusNames=b0867, JW0851;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=8905232; DOI=10.1093/dnares/3.3.137;
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A.,
Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K.,
Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K.,
Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N.,
Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y.,
Yano M., Horiuchi T.;
"A 718-kb DNA sequence of the Escherichia coli K-12 genome
corresponding to the 12.7-28.0 min region on the linkage map.";
DNA Res. 3:137-155(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[4]
X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 18-276 IN COMPLEX WITH ZINC
AND N-ACETYLMURAMOYL-TRIPEPTIDE, COFACTOR, AND ACTIVE SITE.
PubMed=20036252; DOI=10.1016/j.jmb.2009.12.038;
Kerff F., Petrella S., Mercier F., Sauvage E., Herman R., Pennartz A.,
Zervosen A., Luxen A., Frere J.M., Joris B., Charlier P.;
"Specific structural features of the N-acetylmuramoyl-L-alanine
amidase AmiD from Escherichia coli and mechanistic implications for
enzymes of this family.";
J. Mol. Biol. 397:249-259(2010).
-!- CATALYTIC ACTIVITY: Hydrolyzes the link between N-acetylmuramoyl
residues and L-amino acid residues in certain cell-wall
glycopeptides.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000269|PubMed:20036252};
Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:20036252};
-!- SUBCELLULAR LOCATION: Cell outer membrane {ECO:0000305}; Lipid-
anchor {ECO:0000305}.
-!- SIMILARITY: Belongs to the N-acetylmuramoyl-L-alanine amidase 2
family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; U00096; AAC73954.1; -; Genomic_DNA.
EMBL; AP009048; BAA35581.1; -; Genomic_DNA.
PIR; C64825; C64825.
RefSeq; NP_415388.1; NC_000913.3.
RefSeq; WP_001252135.1; NZ_LN832404.1.
PDB; 2BH7; X-ray; 2.20 A; A=18-276.
PDB; 2WKX; X-ray; 1.80 A; A=18-276.
PDB; 3D2Y; X-ray; 1.75 A; A=18-276.
PDB; 3D2Z; X-ray; 2.80 A; A=18-276.
PDBsum; 2BH7; -.
PDBsum; 2WKX; -.
PDBsum; 3D2Y; -.
PDBsum; 3D2Z; -.
ProteinModelPortal; P75820; -.
SMR; P75820; -.
BioGrid; 4259998; 12.
STRING; 316385.ECDH10B_0937; -.
PaxDb; P75820; -.
PRIDE; P75820; -.
EnsemblBacteria; AAC73954; AAC73954; b0867.
EnsemblBacteria; BAA35581; BAA35581; BAA35581.
GeneID; 945494; -.
KEGG; ecj:JW0851; -.
KEGG; eco:b0867; -.
PATRIC; fig|1411691.4.peg.1410; -.
EchoBASE; EB3451; -.
EcoGene; EG13687; amiD.
eggNOG; ENOG4108VBV; Bacteria.
eggNOG; COG3023; LUCA.
HOGENOM; HOG000255964; -.
InParanoid; P75820; -.
KO; K11066; -.
OMA; FRPANYQ; -.
PhylomeDB; P75820; -.
BioCyc; EcoCyc:G6452-MONOMER; -.
BioCyc; MetaCyc:G6452-MONOMER; -.
BRENDA; 3.5.1.28; 2026.
EvolutionaryTrace; P75820; -.
PRO; PR:P75820; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0009279; C:cell outer membrane; IEA:UniProtKB-SubCell.
GO; GO:0019867; C:outer membrane; IDA:EcoliWiki.
GO; GO:0009392; F:N-acetyl-anhydromuramoyl-L-alanine amidase activity; IDA:EcoCyc.
GO; GO:0008745; F:N-acetylmuramoyl-L-alanine amidase activity; IDA:EcoCyc.
GO; GO:0008270; F:zinc ion binding; IDA:EcoliWiki.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0009253; P:peptidoglycan catabolic process; IDA:EcoCyc.
GO; GO:0009254; P:peptidoglycan turnover; IBA:GO_Central.
CDD; cd06583; PGRP; 1.
Gene3D; 1.10.101.10; -; 1.
Gene3D; 3.40.80.10; -; 1.
InterPro; IPR036505; Amidase/PGRP_sf.
InterPro; IPR002502; Amidase_domain.
InterPro; IPR036365; PGBD-like_sf.
InterPro; IPR036366; PGBDSf.
Pfam; PF01510; Amidase_2; 1.
SMART; SM00644; Ami_2; 1.
SUPFAM; SSF47090; SSF47090; 1.
SUPFAM; SSF55846; SSF55846; 1.
PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
1: Evidence at protein level;
3D-structure; Cell outer membrane; Cell wall biogenesis/degradation;
Complete proteome; Hydrolase; Lipoprotein; Membrane; Metal-binding;
Palmitate; Reference proteome; Signal; Zinc.
SIGNAL 1 16 {ECO:0000255|PROSITE-ProRule:PRU00303}.
CHAIN 17 276 N-acetylmuramoyl-L-alanine amidase AmiD.
/FTId=PRO_0000164417.
DOMAIN 42 179 N-acetylmuramoyl-L-alanine amidase.
{ECO:0000255}.
REGION 51 52 Substrate binding.
ACT_SITE 119 119 Proton acceptor.
{ECO:0000269|PubMed:20036252}.
METAL 50 50 Zinc; catalytic.
{ECO:0000269|PubMed:20036252}.
METAL 166 166 Zinc; catalytic.
{ECO:0000269|PubMed:20036252}.
METAL 176 176 Zinc; catalytic.
{ECO:0000269|PubMed:20036252}.
SITE 174 174 Transition state stabilizer.
LIPID 17 17 N-palmitoyl cysteine.
{ECO:0000255|PROSITE-ProRule:PRU00303}.
LIPID 17 17 S-diacylglycerol cysteine.
{ECO:0000255|PROSITE-ProRule:PRU00303}.
STRAND 23 25 {ECO:0000244|PDB:3D2Y}.
STRAND 30 32 {ECO:0000244|PDB:3D2Y}.
STRAND 46 51 {ECO:0000244|PDB:3D2Y}.
HELIX 56 63 {ECO:0000244|PDB:3D2Y}.
STRAND 65 67 {ECO:0000244|PDB:3D2Y}.
STRAND 71 74 {ECO:0000244|PDB:3D2Y}.
HELIX 111 114 {ECO:0000244|PDB:3D2Y}.
STRAND 115 120 {ECO:0000244|PDB:3D2Y}.
STRAND 125 128 {ECO:0000244|PDB:3D2Y}.
STRAND 131 134 {ECO:0000244|PDB:3D2Y}.
HELIX 139 156 {ECO:0000244|PDB:3D2Y}.
HELIX 160 162 {ECO:0000244|PDB:3D2Y}.
STRAND 163 165 {ECO:0000244|PDB:3D2Y}.
HELIX 166 169 {ECO:0000244|PDB:3D2Y}.
TURN 171 173 {ECO:0000244|PDB:3D2Y}.
HELIX 183 188 {ECO:0000244|PDB:3D2Y}.
HELIX 197 204 {ECO:0000244|PDB:3D2Y}.
HELIX 215 225 {ECO:0000244|PDB:3D2Y}.
HELIX 235 249 {ECO:0000244|PDB:3D2Y}.
HELIX 260 273 {ECO:0000244|PDB:3D2Y}.
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


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