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Q2P8P8 (Q2P8P8_XANOM) Unreviewed, UniProtKB/TrEMBL

Last modified February 19, 2014. Version 73. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry infoCustomize order

Names and origin

Protein namesRecommended name:
D-alanine--D-alanine ligase HAMAP-Rule MF_00047

EC=6.3.2.4 HAMAP-Rule MF_00047
Alternative name(s):
D-Ala-D-Ala ligase HAMAP-Rule MF_00047
D-alanylalanine synthetase HAMAP-Rule MF_00047
Gene names
Name:ddl HAMAP-Rule MF_00047
Ordered Locus Names:XOO0324 EMBL BAE67079.1
OrganismXanthomonas oryzae pv. oryzae (strain MAFF 311018) [Complete proteome] [HAMAP]
Taxonomic identifier342109 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas

Protein attributes

Sequence length367 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Cell wall formation By similarity. HAMAP-Rule MF_00047 SAAS SAAS005905

Catalytic activity

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP-Rule MF_00047 SAAS SAAS005905

Cofactor

Binds 2 magnesium or manganese ions per subunit By similarity. HAMAP-Rule MF_00047 SAAS SAAS005905

Pathway

Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP-Rule MF_00047 SAAS SAAS005905

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00047 SAAS SAAS005905.

Sequence similarities

Belongs to the D-alanine--D-alanine ligase family. HAMAP-Rule MF_00047

Contains 1 ATP-grasp domain. HAMAP-Rule MF_00047

Contains ATP-grasp domain. SAAS SAAS005905

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Domain145 – 348204ATP-grasp By similarity HAMAP-Rule MF_00047
Nucleotide binding175 – 23056ATP By similarity HAMAP-Rule MF_00047
Nucleotide binding183 – 1853ADP
Nucleotide binding183 – 1853ATP PDB 3R5F
Nucleotide binding221 – 2244ADP
Nucleotide binding221 – 2244ATP PDB 3R5F

Sites

Metal binding3021Magnesium or manganese 1 By similarity HAMAP-Rule MF_00047
Metal binding3151Magnesium or manganese 1 By similarity HAMAP-Rule MF_00047
Metal binding3151Magnesium or manganese 2 By similarity HAMAP-Rule MF_00047
Metal binding3171Magnesium or manganese 2 By similarity HAMAP-Rule MF_00047
Binding site1411ATP PDB 3R5F
Binding site1921ADP; via amide nitrogen
Binding site1921ATP PDB 3R5F
Binding site2281ADP
Binding site2281ATP PDB 3R5F
Binding site3151ATP PDB 3R5F

Sequences

Sequence LengthMass (Da)Tools
Q2P8P8 [UniParc].

Last modified February 7, 2006. Version 1.
Checksum: 4318A8A5DA76F328

FASTA36739,613
        10         20         30         40         50         60 
MRKIRVGLIF GGKSAEHEVS LQSARNILDA LDPQRFEPVL IGIDKQGQWH VNDPDSFLLH 

        70         80         90        100        110        120 
ADDPARIALH RSGRGVALLP GAQQQQLRPI QPEQALAQID VVFPIVHGTL GEDGSLQGLL 

       130        140        150        160        170        180 
RMANLPFVGS GVLGSAVAMD KDMAKRVLRD ARLAVAPFVC FDRHTAAHAD VDTLIAQLGL 

       190        200        210        220        230        240 
PLFVKPANQG SSVGVSQVRT ADAFAAALAL ALAYDHKVLV EAAVAGREIE CAVLGNAVPH 

       250        260        270        280        290        300 
ASVCGEVVVH DAFYSYATKY ISEHGAEIVI PADIDAQTQQ RIQQIAVQAY QALGCAGMAR 

       310        320        330        340        350        360 
VDVFLCADGR IVINEVNTLP GFTRISMYPK LWQASGLDYR GLITRLIELA LERHTDDQLL 


RSAVELH 

« Hide

References

« Hide 'large scale' references
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AP008229 Genomic DNA. Translation: BAE67079.1.
RefSeqYP_449353.1. NC_007705.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3E5NX-ray2.00A1-367[»]
3R5FX-ray2.07A1-367[»]
3RFCX-ray2.10A1-367[»]
ProteinModelPortalQ2P8P8.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING342109.XOO_0324.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAE67079; BAE67079; BAE67079.
GeneID3856807.
KEGGxom:XOO_0324.
PATRIC24109825. VBIXanOry49434_0366.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG1181.
KOK01921.
OMAMDKIAMK.
OrthoDBEOG64BQ73.
ProtClustDBPRK01966.

Enzyme and pathway databases

BioCycXORY342109:GIX9-329-MONOMER.
UniPathwayUPA00219.

Family and domain databases

Gene3D3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
HAMAPMF_00047. Dala_Dala_lig.
InterProIPR011761. 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]
PANTHERPTHR23132. PTHR23132. 1 hit.
PfamPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
SUPFAMSSF52440. SSF52440. 1 hit.
TIGRFAMsTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ2P8P8.

Entry information

Entry nameQ2P8P8_XANOM
AccessionPrimary (citable) accession number: Q2P8P8
Entry history
Integrated into UniProtKB/TrEMBL: February 7, 2006
Last sequence update: February 7, 2006
Last modified: February 19, 2014
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)