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D5B0W3

- D5B0W3_YERPZ

UniProt

D5B0W3 - D5B0W3_YERPZ

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Protein
D-alanine--D-alanine ligase
Gene
ddl, YPZ3_0535
Organism
Yersinia pestis (strain Z176003)
Status
Unreviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

Cell wall formation By similarity.UniRule annotationSAAS annotations

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotationSAAS annotations

Cofactori

Binds 2 magnesium or manganese ions per subunit By similarity.UniRule annotationSAAS annotations

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi257 – 2571Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi270 – 2701Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi270 – 2701Magnesium or manganese 2 By similarityUniRule annotation
Metal bindingi272 – 2721Magnesium or manganese 2 By similarityUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 18956ATP By similarityUniRule annotation
Add
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. regulation of cell shape Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

LigaseUniRule annotationSAAS annotations

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotations, Peptidoglycan synthesisUniRule annotationSAAS annotations

Keywords - Ligandi

ATP-bindingUniRule annotationSAAS annotations, MagnesiumUniRule annotationSAAS annotations, ManganeseUniRule annotationSAAS annotations, Metal-bindingUniRule annotationSAAS annotations, Nucleotide-binding

Enzyme and pathway databases

BioCyciYPES637386:GKE8-545-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotation (EC:6.3.2.4UniRule annotation)
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene namesi
Name:ddlUniRule annotationImported
Ordered Locus Names:YPZ3_0535Imported
OrganismiYersinia pestis (strain Z176003)Imported
Taxonomic identifieri637386 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
ProteomesiUP000000932: Chromosome

Subcellular locationi

Cytoplasm By similarity UniRule annotationSAAS annotations

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotations

Structurei

3D structure databases

ProteinModelPortaliD5B0W3.
SMRiD5B0W3. Positions 1-306.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini101 – 303203ATP-grasp By similarityUniRule annotation
Add
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.UniRule annotation
Contains ATP-grasp domain.SAAS annotations

Phylogenomic databases

HOGENOMiHOG000011592.
KOiK01921.
OMAiANDTQYR.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR000291. D-Ala_lig_Van_CS.
IPR005905. D_ala_D_ala.
IPR011095. Dala_Dala_lig_C.
IPR011127. Dala_Dala_lig_N.
IPR016185. PreATP-grasp_dom.
[Graphical view]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

D5B0W3-1 [UniParc]FASTAAdd to Basket

« Hide

MAEKVAVLLG GTSAEREVSL LSGQAVLAGL KEAGIDAYGV DTKDFPVTQL    50
KEQGFDKVFI ALHGRGGEDG TLQGVLEFLQ LPYTGSGVMA SALTMDKLRT 100
KLVWQALGLP ISPYVALNRQ QFETLSPEEL VACVAKLGLP LIVKPSHEGS 150
SVGMSKVDHA SELQKALVEA FQHDSDVLIE KWLSGPEFTV AILGDEVLPS 200
IRIQPPGVFY DYDAKYLSDK TQYFCPSGLS DESEQQLAAL ALQAYHALDC 250
SGWGRVDVMQ DRDGHFYLLE VNTSPGMTSH SLVPMAARQY GLSFSQLVAR 300
ILMLAD 306
Length:306
Mass (Da):33,150
Last modified:June 15, 2010 - v1
Checksum:iC78CFF3D2E11F846
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001593 Genomic DNA. Translation: ADE63445.1.
RefSeqiYP_003566707.1. NC_014029.1.

Genome annotation databases

EnsemblBacteriaiADE63445; ADE63445; YPZ3_0535.
GeneIDi8990434.
KEGGiypz:YPZ3_0535.
PATRICi35468335. VBIYerPes97410_0901.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001593 Genomic DNA. Translation: ADE63445.1 .
RefSeqi YP_003566707.1. NC_014029.1.

3D structure databases

ProteinModelPortali D5B0W3.
SMRi D5B0W3. Positions 1-306.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ADE63445 ; ADE63445 ; YPZ3_0535 .
GeneIDi 8990434.
KEGGi ypz:YPZ3_0535.
PATRICi 35468335. VBIYerPes97410_0901.

Phylogenomic databases

HOGENOMi HOG000011592.
KOi K01921.
OMAi ANDTQYR.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci YPES637386:GKE8-545-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi IPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR000291. D-Ala_lig_Van_CS.
IPR005905. D_ala_D_ala.
IPR011095. Dala_Dala_lig_C.
IPR011127. Dala_Dala_lig_N.
IPR016185. PreATP-grasp_dom.
[Graphical view ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Complete genome sequence of Yersinia pestis from new plague natural foci in China."
    Hai R., Yu D., Xia L., Zhu X., Liang Y., Shen X., Zhang E., Zhang H.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: Z176003.
  2. "Complete genome sequences of Yersinia pestis from natural foci in China."
    Shen X., Wang Q., Xia L., Zhu X., Zhang Z., Liang Y., Cai H., Zhang E., Wei J., Chen C., Song Z., Zhang H., Yu D., Hai R.
    J. Bacteriol. 192:3551-3552(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Z176003Imported.

Entry informationi

Entry nameiD5B0W3_YERPZ
AccessioniPrimary (citable) accession number: D5B0W3
Entry historyi
Integrated into UniProtKB/TrEMBL: June 15, 2010
Last sequence update: June 15, 2010
Last modified: June 11, 2014
This is version 30 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome

External Data

Dasty 3

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