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D4ZL38

- D4ZL38_SHEVD

UniProt

D4ZL38 - D4ZL38_SHEVD

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Protein

D-alanine--D-alanine ligase

Gene

ddlA

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.UniRule annotationSAAS annotation

Catalytic activityi

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

Cofactori

Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi283 – 2831Magnesium or manganese 1UniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 1UniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 2UniRule annotation
Metal bindingi298 – 2981Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi154 – 20956ATPUniRule annotationAdd
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. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. regulation of cell shape Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

LigaseUniRule annotationSAAS annotation

Keywords - Biological processi

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

Keywords - Ligandi

ATP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, 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 ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
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 UniRule annotationSAAS annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Structurei

3D structure databases

ProteinModelPortaliD4ZL38.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini124 – 329206ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation
Contains ATP-grasp domain.SAAS annotation

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

        10         20         30         40         50
MSQTNLLLIC GGGGDEHAIS LMSAKFFETS LAKLAHINLL KIELDAQGHY
60 70 80 90 100
RTQAGELCEL TNRKQIRFDD VNKASWPVDY VIPCIHGYPG ETGDIQSYFE
110 120 130 140 150
LIKLPYFGCD SEASRNCFNK VTAKMWFSAL GIPNTPYIFL NDFNDDAINQ
160 170 180 190 200
AQQALASWGS IFIKAASQGS SVGCYRVDSP EELTESLKQA FTYSPYVIVE
210 220 230 240 250
KTIEARELEV AVYEKDGEII ATQPGEIICG TNTFYTFDEK YAENSQAETK
260 270 280 290 300
VVADISESVS QEIREYAVKV FKGMKLSHLS RIDFFLTADN EILLNEINTF
310 320 330
PGLTPISMFP KMLQNHGDNF SDYLNHNIMQ QLSKKD
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 / DSS12Imported.

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: October 29, 2014
This is version 31 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

External Data

Dasty 3