Q87WY7 (DDLB_PSESM) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-alanine--D-alanine ligase B
EC=6.3.2.4

Alternative name(s):
D-Ala-D-Ala ligase B
D-alanylalanine synthetase B

Gene names

Name:	ddlB
Ordered Locus Names:	PSPTO_4406

Organism

Pseudomonas syringae pv. tomato (strain DC3000) [Complete proteome] [HAMAP]

Taxonomic identifier

223283 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas

Protein attributes

Sequence length	319 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

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

Ontologies

Keywords
Biological process	Cell shape Cell wall biogenesis/degradation Peptidoglycan synthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Manganese Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	cellular cell wall organization Inferred from electronic annotation. Source: UniProtKB-KW peptidoglycan biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW 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: UniProtKB-KW D-alanine-D-alanine ligase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 319	319	D-alanine--D-alanine ligase B HAMAP MF_00047		PRO_0000177860
Regions
	Domain	117 – 312	196	ATP-grasp
	Nucleotide binding	143 – 198	56	ATP By similarity
Sites
	Metal binding	266	1	Magnesium or manganese 1 By similarity
	Metal binding	279	1	Magnesium or manganese 1 By similarity
	Metal binding	279	1	Magnesium or manganese 2 By similarity
	Metal binding	281	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q87WY7 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: AD31868A3E161061	FASTA	319	34,087
	10 20 30 40 50 60 MTAVARSSLR STLEPKSFGR VAVLFGGKSA EREVSLNSGN AVLKALLDAG VDAFGIDVGD 70 80 90 100 110 120 DFLQRLVSEK IDRAFIVLHG RGGEDGTMQG LLECLEIPYT GSGVLASALA MDKLRTKQVW 130 140 150 160 170 180 QSLGPATPLH AVLENENDCI CAATELGFPL IVKPAHEGSS IGMAKVNSVD ELIAAWKAAS 190 200 210 220 230 240 TYDSQVLVEQ WIQGPEFTVA SLRGQVLPPI GLGTPHSFYD YDAKYLASDT QYRIPCGLDD 250 260 270 280 290 300 AQEQQLKQLA ARACDAIGIA GWARTDVMQD AEGKFWLLEV NTVPGMTDHS LVPMAARAAG 310 LNFQQLVLAI LADSVQARG

References

[1]

"The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000." Buell C.R., Joardar V., Lindeberg M., Selengut J., Paulsen I.T., Gwinn M.L., Dodson R.J., DeBoy R.T., Durkin A.S., Kolonay J.F., Madupu R., Daugherty S.C., Brinkac L.M., Beanan M.J., Haft D.H., Nelson W.C., Davidsen T.M., Zafar N. , Zhou L., Liu J., Yuan Q., Khouri H.M., Fedorova N.B., Tran B., Russell D., Berry K.J., Utterback T.R., Van Aken S.E., Feldblyum T.V., D'Ascenzo M., Deng W.-L., Ramos A.R., Alfano J.R., Cartinhour S., Chatterjee A.K., Delaney T.P., Lazarowitz S.G., Martin G.B., Schneider D.J., Tang X., Bender C.L., White O., Fraser C.M., Collmer A. Proc. Natl. Acad. Sci. U.S.A. 100:10181-10186(2003) [PubMed: 12928499] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: DC3000.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE016853 Genomic DNA. Translation: AAO57855.1.
RefSeq	NP_794160.1. NC_004578.1.
3D structure databases
ProteinModelPortal	Q87WY7.
SMR	Q87WY7. Positions 19-312.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1186087.
GenomeReviews	Gene locus PSPTO_4406 in contig AE016853_GR.
KEGG	pst:PSPTO_4406.
NMPDR	fig|223283.1.peg.4298.
PATRIC	20000322. VBIPseSyr93040_4521.
TIGR	PSPTO_4406.
Phylogenomic databases
HOGENOM	HBG427092.
OMA	WGRVDAM.
ProtClustDB	PRK01372.
Enzyme and pathway databases
BioCyc	PSYR223283:PSPTO_4406-MONOMER.
Family and domain databases
HAMAP	MF_00047. Dala_Dala_lig. [Tree]
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. IPR013817. Pre-ATP_grasp. IPR016185. PreATP-grasp-like. [Graphical view]
Gene3D	G3DSA:3.30.1490.20. ATP_grasp_subdomain_1. 1 hit. G3DSA:3.30.470.20. ATP_grasp_subdomain_2. 2 hits. G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.
KO	K01921.
PANTHER	PTHR23132. PTHR23132. 1 hit.
Pfam	PF07478. Dala_Dala_lig_C. 1 hit. PF01820. Dala_Dala_lig_N. 2 hits. [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...

Entry information

Entry name

DDLB_PSESM

Accession

Primary (citable) accession number: Q87WY7

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2003
Last modified:	January 25, 2012
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program