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Q2P8P8

- Q2P8P8_XANOM

UniProt

Q2P8P8 - Q2P8P8_XANOM

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Protein
D-alanine--D-alanine ligase
Gene
ddl, XOO0324
Organism
Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
Status
Unreviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

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
Binding sitei141 – 1411ATPImported
Binding sitei192 – 1921ADP; via amide nitrogen
Binding sitei192 – 1921ATPImported
Binding sitei228 – 2281ADP
Binding sitei228 – 2281ATPImported
Metal bindingi302 – 3021Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi315 – 3151Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi315 – 3151Magnesium or manganese 2 By similarityUniRule annotation
Binding sitei315 – 3151ATPImported
Metal bindingi317 – 3171Magnesium or manganese 2 By similarityUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi175 – 23056ATP By similarityUniRule annotation
Add
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. 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 annotationsImported, MagnesiumUniRule annotationSAAS annotations, ManganeseUniRule annotationSAAS annotations, Metal-bindingUniRule annotationSAAS annotations, 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 ligase
D-alanylalanine synthetase
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:XOO0324Imported
OrganismiXanthomonas oryzae pv. oryzae (strain MAFF 311018)
Taxonomic identifieri342109 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
ProteomesiUP000001957: 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

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.

Miscellaneous databases

EvolutionaryTraceiQ2P8P8.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini145 – 348204ATP-grasp By similarityUniRule annotation
Add
BLAST

Sequence similaritiesi

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

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

MRKIRVGLIF GGKSAEHEVS LQSARNILDA LDPQRFEPVL IGIDKQGQWH    50
VNDPDSFLLH ADDPARIALH RSGRGVALLP GAQQQQLRPI QPEQALAQID 100
VVFPIVHGTL GEDGSLQGLL RMANLPFVGS GVLGSAVAMD KDMAKRVLRD 150
ARLAVAPFVC FDRHTAAHAD VDTLIAQLGL PLFVKPANQG SSVGVSQVRT 200
ADAFAAALAL ALAYDHKVLV EAAVAGREIE CAVLGNAVPH ASVCGEVVVH 250
DAFYSYATKY ISEHGAEIVI PADIDAQTQQ RIQQIAVQAY QALGCAGMAR 300
VDVFLCADGR IVINEVNTLP GFTRISMYPK LWQASGLDYR GLITRLIELA 350
LERHTDDQLL RSAVELH 367
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.
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:
EMBL
GenBank
DDBJ
Links Updated
AP008229 Genomic DNA. Translation: BAE67079.1 .
RefSeqi WP_011257296.1. NC_007705.1.
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 311018.
  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: September 3, 2014
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureImported, Complete proteome

External Data

Dasty 3

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