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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
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

Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi268 – 2681Magnesium or manganese 1UniRule annotation
Metal bindingi282 – 2821Magnesium or manganese 1UniRule annotation
Metal bindingi282 – 2821Magnesium or manganese 2UniRule annotation
Metal bindingi284 – 2841Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi146 – 20156ATPUniRule 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

BioCyciXORY342109:GIX9-3659-MONOMER.
UniPathwayiUPA00219.

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:XOO3602Imported
OrganismiXanthomonas oryzae pv. oryzae (strain MAFF 311018)Imported
Taxonomic identifieri342109 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
ProteomesiUP000001957: Chromosome

Subcellular locationi

Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Protein-protein interaction databases

STRINGi342109.XOO_3602.

Structurei

3D structure databases

ProteinModelPortaliQ2NZC0.
SMRiQ2NZC0. Positions 17-316.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini117 – 315199ATP-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

eggNOGiCOG1181.
HOGENOMiHOG000214907.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.

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.

Q2NZC0-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSAVIANART SDPAIFGRVA VLLGGTSSER EVSLNSGSNV LEALRARGVD
60 70 80 90 100
AQPVDGIAAL AKALVAQQFD RVFNVLHGHN GGGEDGIVQG LMEAFGVPYT
110 120 130 140 150
GSDVLGSALS MDKIRTKQVW LSLGLSTPRY ARLAAGASAA DIHVAAQQLG
160 170 180 190 200
LPVIVKPANE GSSVGVSRVF DQAQLEDAVT LAARYDGALL MEQLIEGDEL
210 220 230 240 250
TVAVLGDTAL PSIRIVPKGQ WYDYNAKYIA EDTQYLCPGL EGEPEAQIRQ
260 270 280 290 300
LALDAFRAAG CRGWGRVDVM RDGSSGQLYL LEVNTAPGMT SHSLVPKAAR
310
QLGIDFEELV WRVLEQTL
Length:318
Mass (Da):33,743
Last modified:February 7, 2006 - v1
Checksum:i8E0F1988A5C307F2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008229 Genomic DNA. Translation: BAE70357.1.
RefSeqiWP_011409374.1. NC_007705.1.
YP_452631.1. NC_007705.1.

Genome annotation databases

EnsemblBacteriaiBAE70357; BAE70357; BAE70357.
GeneIDi3859391.
KEGGixom:XOO_3602.
PATRICi24117423. VBIXanOry49434_4110.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008229 Genomic DNA. Translation: BAE70357.1.
RefSeqiWP_011409374.1. NC_007705.1.
YP_452631.1. NC_007705.1.

3D structure databases

ProteinModelPortaliQ2NZC0.
SMRiQ2NZC0. Positions 17-316.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi342109.XOO_3602.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAE70357; BAE70357; BAE70357.
GeneIDi3859391.
KEGGixom:XOO_3602.
PATRICi24117423. VBIXanOry49434_4110.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000214907.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciXORY342109:GIX9-3659-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. "Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity."
    Ochiai H., Inoue Y., Takeya M., Sasaki A., Kaku H.
    Jpn. Agric. Res. Q. 39:275-287(2005)
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MAFF 311018Imported.

Entry informationi

Entry nameiQ2NZC0_XANOM
AccessioniPrimary (citable) accession number: Q2NZC0
Entry historyi
Integrated into UniProtKB/TrEMBL: February 7, 2006
Last sequence update: February 7, 2006
Last modified: February 4, 2015
This is version 75 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.