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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Nitrosococcus watsoni (strain C-113)
Status
Unreviewed-Annotation score: 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

Protein has several cofactor binding sites:
  • Mg2+, Mn2+Note: Binds 2 magnesium or manganese ions per subunit.
  • Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi258 – 2581Magnesium or manganese 1UniRule annotation
Metal bindingi271 – 2711Magnesium or manganese 1UniRule annotation
Metal bindingi271 – 2711Magnesium or manganese 2UniRule annotation
Metal bindingi273 – 2731Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi135 – 19056ATPUniRule 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

BioCyciNWAT105559:GHXU-235-MONOMER.
UniPathwayiUPA00219.
UPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotationSAAS annotation (EC:6.3.2.4UniRule annotationSAAS annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:Nwat_0230Imported
OrganismiNitrosococcus watsoni (strain C-113)Imported
Taxonomic identifieri105559 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaChromatialesChromatiaceaeNitrosococcus
ProteomesiUP000000393 Componenti: 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

ProteinModelPortaliD8K8Z0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini109 – 304196ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

KOiK01921.
OMAiPFLLEMN.

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. 2 hits.
[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.

D8K8Z0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIGRADAKAW GKVAVLMGGY SAEREISLKS GTAVLQALLR QGIEAHGIDV
60 70 80 90 100
GKEVLTQLSK GEFTRAFIVL HGRGGEDGVI QGALETLNLP YTGSGVLGSA
110 120 130 140 150
LTMDKLRSKQ LWRGMDLPTA DFSALTEDTD PAVIAADLGL PLIVKPAREG
160 170 180 190 200
SSLGMMKVES TDALQSAYRE AAIFDTAVFA ERWLSGAEYT AAILADRVLP
210 220 230 240 250
LIRLETPRVF YDFEAKYHAN TTHYFCPCGL SERQEHVLQA LALEAFQVLG
260 270 280 290 300
ASGWGRVDLR CDEKAHPYLL EINTVPGMTD HSLVPMAAQA AGIGFDEMVL
310
RILESSLERR MFQDGA
Length:316
Mass (Da):34,257
Last modified:October 4, 2010 - v1
Checksum:iFB5406A8D7355FA4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002086 Genomic DNA. Translation: ADJ27200.1.
RefSeqiYP_003759521.1. NC_014315.1.

Genome annotation databases

EnsemblBacteriaiADJ27200; ADJ27200; Nwat_0230.
KEGGinwa:Nwat_0230.
PATRICi42232719. VBINitWat28885_0251.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002086 Genomic DNA. Translation: ADJ27200.1.
RefSeqiYP_003759521.1. NC_014315.1.

3D structure databases

ProteinModelPortaliD8K8Z0.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADJ27200; ADJ27200; Nwat_0230.
KEGGinwa:Nwat_0230.
PATRICi42232719. VBINitWat28885_0251.

Phylogenomic databases

KOiK01921.
OMAiPFLLEMN.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciNWAT105559:GHXU-235-MONOMER.

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. 2 hits.
[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]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of chromosome of Nitrosococcus watsoni C-113."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L., Pitluck S., Malfatti S.A., Chain P.S.G., Land M., Hauser L., Kyrpides N., Ivanova N., Cambell M.A., Heidelberg J.F., Klotz M.G., Woyke T.
    Submitted (MAY-2010) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C-113Imported.

Entry informationi

Entry nameiD8K8Z0_NITWC
AccessioniPrimary (citable) accession number: D8K8Z0
Entry historyi
Integrated into UniProtKB/TrEMBL: October 4, 2010
Last sequence update: October 4, 2010
Last modified: March 31, 2015
This is version 31 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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.