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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: 4 out of 5-Experimental evidence at protein leveli

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 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
Binding sitei141 – 1411ATPCombined sources
Binding sitei192 – 1921ATPCombined sources
Binding sitei228 – 2281ATPCombined sources
Metal bindingi302 – 3021Magnesium or manganese 1UniRule annotation
Metal bindingi315 – 3151Magnesium or manganese 1UniRule annotation
Metal bindingi315 – 3151Magnesium or manganese 2UniRule annotation
Binding sitei315 – 3151ATPCombined sources
Metal bindingi317 – 3171Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi175 – 23056ATPUniRule annotationAdd
BLAST
Nucleotide bindingi183 – 1853ATPCombined sources
Nucleotide bindingi221 – 2244ATPCombined sources

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 annotationCombined sources, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding

Enzyme and pathway databases

BioCyciXORY342109:GIX9-329-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:XOO0324Imported
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_0324.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3E5NX-ray2.00A1-367[»]
3R5FX-ray2.07A1-367[»]
3RFCX-ray2.10A1-367[»]
ProteinModelPortaliQ2P8P8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ2P8P8.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini145 – 348204ATP-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

eggNOGiCOG1181.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

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.

Q2P8P8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRKIRVGLIF GGKSAEHEVS LQSARNILDA LDPQRFEPVL IGIDKQGQWH
60 70 80 90 100
VNDPDSFLLH ADDPARIALH RSGRGVALLP GAQQQQLRPI QPEQALAQID
110 120 130 140 150
VVFPIVHGTL GEDGSLQGLL RMANLPFVGS GVLGSAVAMD KDMAKRVLRD
160 170 180 190 200
ARLAVAPFVC FDRHTAAHAD VDTLIAQLGL PLFVKPANQG SSVGVSQVRT
210 220 230 240 250
ADAFAAALAL ALAYDHKVLV EAAVAGREIE CAVLGNAVPH ASVCGEVVVH
260 270 280 290 300
DAFYSYATKY ISEHGAEIVI PADIDAQTQQ RIQQIAVQAY QALGCAGMAR
310 320 330 340 350
VDVFLCADGR IVINEVNTLP GFTRISMYPK LWQASGLDYR GLITRLIELA
360
LERHTDDQLL RSAVELH
Length:367
Mass (Da):39,613
Last modified:February 7, 2006 - v1
Checksum:i4318A8A5DA76F328
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008229 Genomic DNA. Translation: BAE67079.1.
RefSeqiWP_011257296.1. NC_007705.1.
YP_449353.1. NC_007705.1.

Genome annotation databases

EnsemblBacteriaiBAE67079; BAE67079; BAE67079.
GeneIDi3856807.
KEGGixom:XOO_0324.
PATRICi24109825. VBIXanOry49434_0366.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008229 Genomic DNA. Translation: BAE67079.1.
RefSeqiWP_011257296.1. NC_007705.1.
YP_449353.1. NC_007705.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3E5NX-ray2.00A1-367[»]
3R5FX-ray2.07A1-367[»]
3RFCX-ray2.10A1-367[»]
ProteinModelPortaliQ2P8P8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi342109.XOO_0324.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAE67079; BAE67079; BAE67079.
GeneIDi3856807.
KEGGixom:XOO_0324.
PATRICi24109825. VBIXanOry49434_0366.

Phylogenomic databases

eggNOGiCOG1181.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciXORY342109:GIX9-329-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ2P8P8.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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.
  2. "Crystal strucutre of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331."
    Doan T.N.T., Kim J.K., Kim H.S., Ahn Y.J., Kim J.G., Lee B.M., Kang L.W.
    Submitted (AUG-2008) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS).
  3. "Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ATP."
    Doan T.T.N., Kim J.K., Kang L.W.
    Submitted (MAR-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) IN COMPLEX WITH ATP.
  4. "Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP."
    Doan T.T.N., Kim J.K., Ahn Y.J., Kang L.W.
    Submitted (APR-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH ADP.

Entry informationi

Entry nameiQ2P8P8_XANOM
AccessioniPrimary (citable) accession number: Q2P8P8
Entry historyi
Integrated into UniProtKB/TrEMBL: February 7, 2006
Last sequence update: February 7, 2006
Last modified: March 4, 2015
This is version 82 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, 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.