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D4ZL38

- D4ZL38_SHEVD

UniProt

D4ZL38 - D4ZL38_SHEVD

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Protein
D-alanine--D-alanine ligase
Gene
ddlA, ddl, SVI_2416
Organism
Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12)
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 bindingi283 – 2831Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 2 By similarityUniRule annotation
Metal bindingi298 – 2981Magnesium or manganese 2 By similarityUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi154 – 20956ATP 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 annotationsImported

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

BioCyciSVIO637905:GCRO-2518-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:ddlAImported
Synonyms:ddlUniRule annotationImported
Ordered Locus Names:SVI_2416Imported
OrganismiShewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12)Imported
Taxonomic identifieri637905 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
ProteomesiUP000002350: 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

ProteinModelPortaliD4ZL38.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini124 – 329206ATP-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.
OMAiQIDVIFP.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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.

D4ZL38-1 [UniParc]FASTAAdd to Basket

« Hide

MSQTNLLLIC GGGGDEHAIS LMSAKFFETS LAKLAHINLL KIELDAQGHY    50
RTQAGELCEL TNRKQIRFDD VNKASWPVDY VIPCIHGYPG ETGDIQSYFE 100
LIKLPYFGCD SEASRNCFNK VTAKMWFSAL GIPNTPYIFL NDFNDDAINQ 150
AQQALASWGS IFIKAASQGS SVGCYRVDSP EELTESLKQA FTYSPYVIVE 200
KTIEARELEV AVYEKDGEII ATQPGEIICG TNTFYTFDEK YAENSQAETK 250
VVADISESVS QEIREYAVKV FKGMKLSHLS RIDFFLTADN EILLNEINTF 300
PGLTPISMFP KMLQNHGDNF SDYLNHNIMQ QLSKKD 336
Length:336
Mass (Da):37,711
Last modified:June 15, 2010 - v1
Checksum:i3A02D07EBF5F1C27
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP011177 Genomic DNA. Translation: BAJ02387.1.
RefSeqiWP_013051691.1. NC_014012.1.
YP_003557165.1. NC_014012.1.

Genome annotation databases

EnsemblBacteriaiBAJ02387; BAJ02387; SVI_2416.
GeneIDi8966618.
KEGGisvo:SVI_2416.
PATRICi35461075. VBISheVio92117_2333.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP011177 Genomic DNA. Translation: BAJ02387.1 .
RefSeqi WP_013051691.1. NC_014012.1.
YP_003557165.1. NC_014012.1.

3D structure databases

ProteinModelPortali D4ZL38.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAJ02387 ; BAJ02387 ; SVI_2416 .
GeneIDi 8966618.
KEGGi svo:SVI_2416.
PATRICi 35461075. VBISheVio92117_2333.

Phylogenomic databases

HOGENOMi HOG000011592.
KOi K01921.
OMAi QIDVIFP.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci SVIO637905:GCRO-2518-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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

  1. "Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments."
    Aono E., Baba T., Ara T., Nishi T., Nakamichi T., Inamoto E., Toyonaga H., Hasegawa M., Takai Y., Okumura Y., Baba M., Tomita M., Kato C., Oshima T., Nakasone K., Mori H.
    Mol. Biosyst. 6:1216-1226(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCM 10179 / CIP 106290 / LMG 19151 / DSS12.

Entry informationi

Entry nameiD4ZL38_SHEVD
AccessioniPrimary (citable) accession number: D4ZL38
Entry historyi
Integrated into UniProtKB/TrEMBL: June 15, 2010
Last sequence update: June 15, 2010
Last modified: September 3, 2014
This is version 29 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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