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Q2P8P8

- Q2P8P8_XANOM

UniProt

Q2P8P8 - Q2P8P8_XANOM

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
Status
Unreviewed - Annotation score: 3 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

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei141 – 1411ATPImported
Binding sitei192 – 1921ADP; via amide nitrogen
Binding sitei192 – 1921ATPImported
Binding sitei228 – 2281ADP
Binding sitei228 – 2281ATPImported
Metal bindingi302 – 3021Magnesium or manganese 1UniRule annotation
Metal bindingi315 – 3151Magnesium or manganese 1UniRule annotation
Metal bindingi315 – 3151Magnesium or manganese 2UniRule annotation
Binding sitei315 – 3151ATPImported
Metal bindingi317 – 3171Magnesium or manganese 2UniRule annotation

Regions

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

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:GIX9-329-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: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:
PDBe
RCSB PDB
PDBj
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
Contains ATP-grasp domain.SAAS annotation

Phylogenomic databases

eggNOGiCOG1181.
KOiK01921.
OMAiQIDVIFP.
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:
EMBL
GenBank
DDBJ
Links Updated
AP008229 Genomic DNA. Translation: BAE67079.1.
RefSeqiYP_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:
EMBL
GenBank
DDBJ
Links Updated
AP008229 Genomic DNA. Translation: BAE67079.1 .
RefSeqi YP_449353.1. NC_007705.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3E5N X-ray 2.00 A 1-367 [» ]
3R5F X-ray 2.07 A 1-367 [» ]
3RFC X-ray 2.10 A 1-367 [» ]
ProteinModelPortali Q2P8P8.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 342109.XOO_0324.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAE67079 ; BAE67079 ; BAE67079 .
GeneIDi 3856807.
KEGGi xom:XOO_0324.
PATRICi 24109825. VBIXanOry49434_0366.

Phylogenomic databases

eggNOGi COG1181.
KOi K01921.
OMAi QIDVIFP.
OrthoDBi EOG64BQ73.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci XORY342109:GIX9-329-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q2P8P8.

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

« 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: October 29, 2014
This is version 78 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureImported, Complete proteomeImported

External Data

Dasty 3