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P75820

- AMID_ECOLI

UniProt

P75820 - AMID_ECOLI

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Protein
N-acetylmuramoyl-L-alanine amidase AmiD
Gene
amiD, ybjR, b0867, JW0851
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.

Cofactori

Binds 1 zinc ion per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi50 – 501Zinc; catalytic
Active sitei119 – 1191Proton acceptor1 Publication
Metal bindingi166 – 1661Zinc; catalytic
Sitei174 – 1741Transition state stabilizer
Metal bindingi176 – 1761Zinc; catalytic

GO - Molecular functioni

  1. N-acetyl-anhydromuramoyl-L-alanine amidase activity Source: EcoCyc
  2. N-acetylmuramoyl-L-alanine amidase activity Source: EcoCyc
  3. zinc ion binding Source: EcoliWiki

GO - Biological processi

  1. peptidoglycan catabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Cell wall biogenesis/degradation

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:G6452-MONOMER.
ECOL316407:JW0851-MONOMER.
MetaCyc:G6452-MONOMER.
RETL1328306-WGS:GSTH-2906-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
N-acetylmuramoyl-L-alanine amidase AmiD (EC:3.5.1.28)
Gene namesi
Name:amiD
Synonyms:ybjR
Ordered Locus Names:b0867, JW0851
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG13687. amiD.

Subcellular locationi

GO - Cellular componenti

  1. cell outer membrane Source: UniProtKB-SubCell
  2. outer membrane Source: EcoliWiki
Complete GO annotation...

Keywords - Cellular componenti

Cell outer membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1616 By similarity
Add
BLAST
Chaini17 – 276260N-acetylmuramoyl-L-alanine amidase AmiD
PRO_0000164417Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi17 – 171N-palmitoyl cysteine By similarity
Lipidationi17 – 171S-diacylglycerol cysteine By similarity

Keywords - PTMi

Lipoprotein, Palmitate

Proteomic databases

PRIDEiP75820.

Expressioni

Gene expression databases

GenevestigatoriP75820.

Interactioni

Protein-protein interaction databases

STRINGi511145.b0867.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi23 – 253
Beta strandi30 – 323
Beta strandi46 – 516
Helixi56 – 638
Beta strandi65 – 673
Beta strandi71 – 744
Helixi111 – 1144
Beta strandi115 – 1206
Beta strandi125 – 1284
Beta strandi131 – 1344
Helixi139 – 15618
Helixi160 – 1623
Beta strandi163 – 1653
Helixi166 – 1694
Turni171 – 1733
Helixi183 – 1886
Helixi197 – 2048
Helixi215 – 22511
Helixi235 – 24915
Helixi260 – 27314

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BH7X-ray2.20A18-276[»]
2WKXX-ray1.80A18-276[»]
3D2YX-ray1.75A18-276[»]
3D2ZX-ray2.80A18-276[»]
ProteinModelPortaliP75820.

Miscellaneous databases

EvolutionaryTraceiP75820.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni51 – 522Substrate binding

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG3023.
HOGENOMiHOG000255964.
KOiK11066.
OMAiIGAWPDE.
OrthoDBiEOG60GRR5.
PhylomeDBiP75820.

Family and domain databases

Gene3Di3.40.80.10. 1 hit.
InterProiIPR002502. Amidase_domain.
IPR002477. Peptidoglycan-bd-like.
[Graphical view]
PfamiPF01510. Amidase_2. 1 hit.
[Graphical view]
SMARTiSM00644. Ami_2. 1 hit.
[Graphical view]
SUPFAMiSSF47090. SSF47090. 1 hit.
SSF55846. SSF55846. 1 hit.
PROSITEiPS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P75820-1 [UniParc]FASTAAdd to Basket

« Hide

MRRFFWLVAA ALLLAGCAGE KGIVEKEGYQ LDTRRQAQAA YPRIKVLVIH    50
YTADDFDSSL ATLTDKQVSS HYLVPAVPPR YNGKPRIWQL VPEQELAWHA 100
GISAWRGATR LNDTSIGIEL ENRGWQKSAG VKYFAPFEPA QIQALIPLAK 150
DIIARYHIKP ENVVAHADIA PQRKDDPGPL FPWQQLAQQG IGAWPDAQRV 200
NFYLAGRAPH TPVDTASLLE LLARYGYDVK PDMTPREQRR VIMAFQMHFR 250
PTLYNGEADA ETQAIAEALL EKYGQD 276
Length:276
Mass (Da):31,072
Last modified:February 1, 1997 - v1
Checksum:iE6E4F642AFF548CD
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00096 Genomic DNA. Translation: AAC73954.1.
AP009048 Genomic DNA. Translation: BAA35581.1.
PIRiC64825.
RefSeqiNP_415388.1. NC_000913.3.
YP_489140.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73954; AAC73954; b0867.
BAA35581; BAA35581; BAA35581.
GeneIDi12931004.
945494.
KEGGiecj:Y75_p0840.
eco:b0867.
PATRICi32116941. VBIEscCol129921_0896.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00096 Genomic DNA. Translation: AAC73954.1 .
AP009048 Genomic DNA. Translation: BAA35581.1 .
PIRi C64825.
RefSeqi NP_415388.1. NC_000913.3.
YP_489140.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2BH7 X-ray 2.20 A 18-276 [» ]
2WKX X-ray 1.80 A 18-276 [» ]
3D2Y X-ray 1.75 A 18-276 [» ]
3D2Z X-ray 2.80 A 18-276 [» ]
ProteinModelPortali P75820.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 511145.b0867.

Proteomic databases

PRIDEi P75820.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73954 ; AAC73954 ; b0867 .
BAA35581 ; BAA35581 ; BAA35581 .
GeneIDi 12931004.
945494.
KEGGi ecj:Y75_p0840.
eco:b0867.
PATRICi 32116941. VBIEscCol129921_0896.

Organism-specific databases

EchoBASEi EB3451.
EcoGenei EG13687. amiD.

Phylogenomic databases

eggNOGi COG3023.
HOGENOMi HOG000255964.
KOi K11066.
OMAi IGAWPDE.
OrthoDBi EOG60GRR5.
PhylomeDBi P75820.

Enzyme and pathway databases

BioCyci EcoCyc:G6452-MONOMER.
ECOL316407:JW0851-MONOMER.
MetaCyc:G6452-MONOMER.
RETL1328306-WGS:GSTH-2906-MONOMER.

Miscellaneous databases

EvolutionaryTracei P75820.
PROi P75820.

Gene expression databases

Genevestigatori P75820.

Family and domain databases

Gene3Di 3.40.80.10. 1 hit.
InterProi IPR002502. Amidase_domain.
IPR002477. Peptidoglycan-bd-like.
[Graphical view ]
Pfami PF01510. Amidase_2. 1 hit.
[Graphical view ]
SMARTi SM00644. Ami_2. 1 hit.
[Graphical view ]
SUPFAMi SSF47090. SSF47090. 1 hit.
SSF55846. SSF55846. 1 hit.
PROSITEi PS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view ]
ProtoNeti Search...

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. "Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family."
    Kerff F., Petrella S., Mercier F., Sauvage E., Herman R., Pennartz A., Zervosen A., Luxen A., Frere J.M., Joris B., Charlier P.
    J. Mol. Biol. 397:249-259(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 18-276 IN COMPLEX WITH ZINC AND N-ACETYLMURAMOYL-TRIPEPTIDE, COFACTOR, ACTIVE SITE.

Entry informationi

Entry nameiAMID_ECOLI
AccessioniPrimary (citable) accession number: P75820
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: February 1, 1997
Last modified: July 9, 2014
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

External Data

Dasty 3

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