D-alanine--D-alanine ligase - Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

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Q2P8P8 (Q2P8P8_XANOM) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 67. History...

Clusters with 100%, 90%, 50% identity |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info Customize order

Names and origin

Protein names

Recommended 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

Organism

Xanthomonas oryzae pv. oryzae (strain MAFF 311018) [Complete proteome] [HAMAP]

Taxonomic identifier

342109 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Xanthomonadales › Xanthomonadaceae › Xanthomonas ›

Protein attributes

Sequence length	367 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cell wall formation By similarity. SAAS SAAS005905 HAMAP-Rule MF_00047
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. SAAS SAAS005905 HAMAP-Rule MF_00047
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity. SAAS SAAS005905 HAMAP-Rule MF_00047
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. SAAS SAAS005905 HAMAP-Rule MF_00047
Subcellular location	Cytoplasm By similarity SAAS SAAS005905 HAMAP-Rule MF_00047.
Sequence similarities	Belongs to the D-alanine--D-alanine ligase family. HAMAP-Rule MF_00047 Contains 1 ATP-grasp domain. SAAS SAAS005905 HAMAP-Rule MF_00047

Ontologies

Keywords
Biological process	Cell shape Cell wall biogenesis/degradation SAAS SAAS005905 HAMAP-Rule MF_00047 Peptidoglycan synthesis SAAS SAAS005905 HAMAP-Rule MF_00047
Cellular component	Cytoplasm SAAS SAAS005905 HAMAP-Rule MF_00047
Ligand	ATP-binding SAAS SAAS005905 HAMAP-Rule MF_00047 PDB 3R5F Magnesium SAAS SAAS005905 HAMAP-Rule MF_00047 Manganese SAAS SAAS005905 HAMAP-Rule MF_00047 Metal-binding SAAS SAAS005905 HAMAP-Rule MF_00047 Nucleotide-binding
Molecular function	Ligase SAAS SAAS005905 HAMAP-Rule MF_00047 EMBL BAE67079.1
Technical term	3D-structure PDB 3E5N PDB 3RFC PDB 3R5F Complete proteome
Gene Ontology (GO)
Biological_process	peptidoglycan biosynthetic process Inferred from electronic annotation. Source: HAMAP regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cell wall Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP D-alanine-D-alanine ligase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Regions

Domain

145 – 348

204

ATP-grasp By similarity HAMAP-Rule MF_00047

Nucleotide binding

175 – 230

ATP By similarity HAMAP-Rule MF_00047

Nucleotide binding

183 – 185

ADP

Nucleotide binding

183 – 185

ATP PDB 3R5F

Nucleotide binding

221 – 224

ADP

Nucleotide binding

221 – 224

ATP PDB 3R5F

Sites

Metal binding

302

Magnesium or manganese 1 By similarity HAMAP-Rule MF_00047

Metal binding

315

Magnesium or manganese 1 By similarity HAMAP-Rule MF_00047

Metal binding

315

Magnesium or manganese 2 By similarity HAMAP-Rule MF_00047

Metal binding

317

Magnesium or manganese 2 By similarity HAMAP-Rule MF_00047

Binding site

141

ATP PDB 3R5F

Binding site

192

ADP; via amide nitrogen

Binding site

192

ATP PDB 3R5F

Binding site

228

ADP

Binding site

228

ATP PDB 3R5F

Binding site

315

ATP PDB 3R5F

Sequences

Sequence

Length

Mass (Da)

Tools

Q2P8P8 [UniParc].

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

367

39,613

        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' referencesShow '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.

RefSeq

YP_449353.1. NC_007705.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q2P8P8.

ModBase

Search...

Protein-protein interaction databases

STRING

342109.XOO_0324.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAE67079; BAE67079; BAE67079.

GeneID

3856807.

KEGG

xom:XOO_0324.

PATRIC

24109825. VBIXanOry49434_0366.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG1181.

K01921.

OMA

LLHGPFG.

ProtClustDB

PRK01966.

Enzyme and pathway databases

UniPathway

UPA00219.

Family and domain databases

Gene3D

3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.

HAMAP

MF_00047. Dala_Dala_lig.

InterPro

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]

PANTHER

PTHR23132. PTHR23132. 1 hit.

Pfam

PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]

SUPFAM

SSF52440. PreATP-grasp-like. 1 hit.

TIGRFAMs

TIGR01205. D_ala_D_alaTIGR. 1 hit.

PROSITE

PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q2P8P8.

Entry information

Entry name

Q2P8P8_XANOM

Accession

Primary (citable) accession number: Q2P8P8

Entry history

Integrated into UniProtKB/TrEMBL:	February 7, 2006
Last sequence update:	February 7, 2006
Last modified:	May 1, 2013
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information