Reviewed, UniProtKB/Swiss-Prot Q89GA7 (DDLA_BRAJA)

Names and origin

Protein names

Recommended name:
    D-alanine--D-alanine ligase A
    EC=6.3.2.4
Alternative name(s):
    D-alanylalanine synthase A
    D-Ala-D-Ala ligase A

Gene names

Name:	ddlA
Ordered Locus Names:	blr6438

Organism

Bradyrhizobium japonicum [Complete proteome] [HAMAP]

Taxonomic identifier

375 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium

Protein attributes

Sequence length	373 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	Cell wall formation By similarity.
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity.
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis.
Subcellular location	CytoplasmBy similarity.
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	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: HAMAP
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro D-alanine-D-alanine ligase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese 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 – 373	373	D-alanine--D-alanine ligase A		PRO_0000177792
Regions
	Domain	146 – 355	210	ATP-grasp
	Nucleotide binding	179 – 234	56	ATP By similarity
Sites
	Metal binding	308	1	Magnesium or manganese 1 By similarity
	Metal binding	322	1	Magnesium or manganese 1 By similarity
	Metal binding	322	1	Magnesium or manganese 2 By similarity
	Metal binding	324	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q89GA7-1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 896E99143E48A84C	FASTA	373	40,799
	10 20 30 40 50 60 MADKIRVVVL YGGRSGEHEV SLKSAASVFR HLDRTRFEVI PVSIDKTGRW QWNDLRSLDQ 70 80 90 100 110 120 AHAAALPILP DAPEMRLARG PDGRGVLVPI TQGAAAPIAI DVVFPVIHGP LCEDGTVQGL 130 140 150 160 170 180 LELADVAYVG SGVLASAVSM DKDVAKRLAE FAGIPVAPYR VLTRKAFVQD RVSSLAKAVE 190 200 210 220 230 240 GLSLPVFVKP CNMGSSVGIH KVKTQDALEA ALDDAFRYDV KVLVQQGIDA REIEVAVLED 250 260 270 280 290 300 ETLFASLASE LNPNAHHEFY SYEAKYLDPD GARVDLPARL DAAQMERVRS LATRVFAALE 310 320 330 340 350 360 CSGFARVDFF LDRKTGEFCF NEINTLPGFT SISMYPKMME ASGVPYGELL SRLVDLALDR 370 HRQRQSLERG YAS

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
EMBLGenBankDDBJ	BA000040 Genomic DNA. Translation: BAC51703.1.
RefSeq	NP_773078.1.
3D structure databases
HSSP	HSSP built from PDB template 1IOW based on UniProtKB P07862.
ModBase	Search...
Genome annotation databases
GeneID	1047518.
GenomeReviews	Gene locus blr6438 in contig BA000040_GR.
KEGG	bja:blr6438.
NMPDR	fig|224911.1.peg.6438.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q89GA7.
Enzyme and pathway databases
BioCyc	BJAP224911:BLR6438-MON.
Family and domain databases
HAMAP	MF_00047. [Tree]
InterPro	IPR011761. ATP-grasp. 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. [Graphical view]
Gene3D	G3DSA:3.30.470.20. ATP_grasp_subdomain_2. 1 hit. G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.
Pfam	PF07478. Dala_Dala_lig_C. 1 hit. PF01820. Dala_Dala_lig_N. 1 hit. [Graphical view]
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

DDLA_BRAJA

Accession

Primary (citable) accession number: Q89GA7

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2003
Last modified:	November 25, 2008
This is version 42 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)