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I3V097

- I3V097_PSEPU

UniProt

I3V097 - I3V097_PSEPU

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Protein

D-alanine--D-alanine ligase

Gene
ddl, YSA_08133
Organism
Pseudomonas putida ND6
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 bindingi208 – 2081Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi221 – 2211Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi221 – 2211Magnesium or manganese 2 By similarityUniRule annotation
Metal bindingi223 – 2231Magnesium or manganese 2 By similarityUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi78 – 13356ATP By similarityUniRule 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. 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

BioCyciPPUT231023:GLIT-4469-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 annotation
ORF Names:YSA_08133Imported
OrganismiPseudomonas putida ND6Imported
Taxonomic identifieri231023 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000005268: 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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini51 – 254204ATP-grasp By similarityUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

KOiK01921.

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.

I3V097-1 [UniParc]FASTAAdd to Basket

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MEIGIDLLFP ALHGRWGEDG TIQGLAAMCG LPCVGSGVLG SAMAMDKDVT    50
KRMVQSAGLV VGPWLALNSM RPWEELVECL GSSTLFVKPA TSGSSIGVSR 100
VSNALEYAAA FAIAAREDTK VLVEAAVCGR EIECGVLELE EGLMASVVGE 150
IIKKEGHAYY DYQAKYDSNS VTGLRVPSLL PPDIVARIQA LSVQAFRCLE 200
LKGYARVDFF LTEEGEIILN EINTLPGFTS ASMYPKMFEC SGYPPPKLVG 250
ALVEYGLSSA SKERL 265
Length:265
Mass (Da):28,381
Last modified:September 5, 2012 - v1
Checksum:i50718CCDD9E10ACF
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP003588 Genomic DNA. Translation: AFK71168.1.
RefSeqiWP_014755786.1. NC_017986.1.
YP_006388283.1. NC_017986.1.

Genome annotation databases

EnsemblBacteriaiAFK71168; AFK71168; YSA_08133.
GeneIDi12993400.
KEGGippi:YSA_08133.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP003588 Genomic DNA. Translation: AFK71168.1 .
RefSeqi WP_014755786.1. NC_017986.1.
YP_006388283.1. NC_017986.1.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AFK71168 ; AFK71168 ; YSA_08133 .
GeneIDi 12993400.
KEGGi ppi:YSA_08133.

Phylogenomic databases

KOi K01921.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci PPUT231023:GLIT-4469-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 of the Naphthalene-Degrading Pseudomonas putida Strain ND6."
    Li S., Zhao H., Li Y., Niu S., Cai B.
    J. Bacteriol. 194:5154-5155(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ND6Imported.

Entry informationi

Entry nameiI3V097_PSEPU
AccessioniPrimary (citable) accession number: I3V097
Entry historyi
Integrated into UniProtKB/TrEMBL: September 5, 2012
Last sequence update: September 5, 2012
Last modified: September 3, 2014
This is version 14 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