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Protein

N-acetylmuramoyl-L-alanine amidase AmiD

Gene

amiD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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

Zn2+1 PublicationNote: Binds 1 zinc ion per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi50 – 501Zinc; catalytic1 Publication
Active sitei119 – 1191Proton acceptor1 Publication
Metal bindingi166 – 1661Zinc; catalytic1 Publication
Sitei174 – 1741Transition state stabilizer
Metal bindingi176 – 1761Zinc; catalytic1 Publication

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. cell wall organization Source: UniProtKB-KW
  2. 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 – 1616PROSITE-ProRule annotationAdd
BLAST
Chaini17 – 276260N-acetylmuramoyl-L-alanine amidase AmiDPRO_0000164417Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi17 – 171N-palmitoyl cysteinePROSITE-ProRule annotation
Lipidationi17 – 171S-diacylglycerol cysteinePROSITE-ProRule annotation

Keywords - PTMi

Lipoprotein, Palmitate

Proteomic databases

PRIDEiP75820.

Expressioni

Gene expression databases

GenevestigatoriP75820.

Interactioni

Protein-protein interaction databases

STRINGi511145.b0867.

Structurei

Secondary structure

1
276
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi23 – 253Combined sources
Beta strandi30 – 323Combined sources
Beta strandi46 – 516Combined sources
Helixi56 – 638Combined sources
Beta strandi65 – 673Combined sources
Beta strandi71 – 744Combined sources
Helixi111 – 1144Combined sources
Beta strandi115 – 1206Combined sources
Beta strandi125 – 1284Combined sources
Beta strandi131 – 1344Combined sources
Helixi139 – 15618Combined sources
Helixi160 – 1623Combined sources
Beta strandi163 – 1653Combined sources
Helixi166 – 1694Combined sources
Turni171 – 1733Combined sources
Helixi183 – 1886Combined sources
Helixi197 – 2048Combined sources
Helixi215 – 22511Combined sources
Helixi235 – 24915Combined sources
Helixi260 – 27314Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BH7X-ray2.20A18-276[»]
2WKXX-ray1.80A18-276[»]
3D2YX-ray1.75A18-276[»]
3D2ZX-ray2.80A18-276[»]
ProteinModelPortaliP75820.
SMRiP75820. Positions 20-276.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP75820.

Family & Domainsi

Region

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

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG3023.
HOGENOMiHOG000255964.
InParanoidiP75820.
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

        10         20         30         40         50
MRRFFWLVAA ALLLAGCAGE KGIVEKEGYQ LDTRRQAQAA YPRIKVLVIH
60 70 80 90 100
YTADDFDSSL ATLTDKQVSS HYLVPAVPPR YNGKPRIWQL VPEQELAWHA
110 120 130 140 150
GISAWRGATR LNDTSIGIEL ENRGWQKSAG VKYFAPFEPA QIQALIPLAK
160 170 180 190 200
DIIARYHIKP ENVVAHADIA PQRKDDPGPL FPWQQLAQQG IGAWPDAQRV
210 220 230 240 250
NFYLAGRAPH TPVDTASLLE LLARYGYDVK PDMTPREQRR VIMAFQMHFR
260 270
PTLYNGEADA ETQAIAEALL EKYGQD
Length:276
Mass (Da):31,072
Last modified:February 1, 1997 - v1
Checksum:iE6E4F642AFF548CD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BH7X-ray2.20A18-276[»]
2WKXX-ray1.80A18-276[»]
3D2YX-ray1.75A18-276[»]
3D2ZX-ray2.80A18-276[»]
ProteinModelPortaliP75820.
SMRiP75820. Positions 20-276.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi511145.b0867.

Proteomic databases

PRIDEiP75820.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EchoBASEiEB3451.
EcoGeneiEG13687. amiD.

Phylogenomic databases

eggNOGiCOG3023.
HOGENOMiHOG000255964.
InParanoidiP75820.
KOiK11066.
OMAiIGAWPDE.
OrthoDBiEOG60GRR5.
PhylomeDBiP75820.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP75820.
PROiP75820.

Gene expression databases

GenevestigatoriP75820.

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]
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. "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: January 7, 2015
This is version 118 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

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 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.