Q89PS5 (DDLB_BRAJA) 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:	ddlA
Synonyms:	ddlB
Ordered Locus Names:	blr3405

Organism

Bradyrhizobium japonicum

Taxonomic identifier

375 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium

Protein attributes

Sequence length	376 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 Reference 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 – 376	376	D-alanine--D-alanine ligase B HAMAP MF_00047		PRO_0000177793
Regions
	Domain	155 – 361	207	ATP-grasp
	Nucleotide binding	184 – 239	56	ATP By similarity
Sites
	Metal binding	316	1	Magnesium or manganese 1 By similarity
	Metal binding	328	1	Magnesium or manganese 1 By similarity
	Metal binding	328	1	Magnesium or manganese 2 By similarity
	Metal binding	330	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q89PS5 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: ADF689A391337460	FASTA	376	39,991
	10 20 30 40 50 60 MTAYGGEMTK ERRKITVGLL FGGRSAEHEV SRASAANILR ALNSDRYDVY LIGISRDGRW 70 80 90 100 110 120 FACDSGNGAG TGSTALTISD EAPEIGLVPG GRGRLVHCDG PTGSDAGSID VAFPILHGPN 130 140 150 160 170 180 GEDGTVQGAL ELADVSFVGS SVTGSAVAMD KEVSKRLMRD AGLPVVPFLT TTASSRIEYA 190 200 210 220 230 240 AAVAALGTPD LFVKPANLGS SVGVSRARSE EEFAASCALA FRYDRKILVE QALNGAREIE 250 260 270 280 290 300 CSVLEESTGD IRASGLGEIV RASEHGFYSY QAKYIDADGA ALHIPADLPL LQARRLQELA 310 320 330 340 350 360 VEVFNVLCCE GMARVDFFVQ GDEVFVNEAN TLPGFTSSSM YPKLWEASGL SQTDLMDKLI 370 AHAFARHERR RALSFG

References

[1]

"Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110." Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S. DNA Res. 9:189-197(2002) [PubMed: 12597275] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: USDA 110.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000040 Genomic DNA. Translation: BAC48670.1.
RefSeq	NP_770045.1. NC_004463.1.
3D structure databases
ProteinModelPortal	Q89PS5.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1050703.
GenomeReviews	Gene locus blr3405 in contig BA000040_GR.
KEGG	bja:blr3405.
NMPDR	fig|224911.1.peg.3405.
PATRIC	21190303. VBIBraJap65052_3409.
Phylogenomic databases
HOGENOM	HBG427092.
OMA	CKAINAY.
PhylomeDB	Q89PS5.
ProtClustDB	PRK01966.
Enzyme and pathway databases
BioCyc	BJAP224911:BLR3405-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. 1 hit. 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. 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...

Entry information

Entry name

DDLB_BRAJA

Accession

Primary (citable) accession number: Q89PS5

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2003
Last modified:	January 25, 2012
This is version 59 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program