Reviewed, UniProtKB/Swiss-Prot Q98JS0 (DDLA_RHILO)

Names and origin

Protein names

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

Gene names

Name:	ddlA
Ordered Locus Names:	mll1812

Organism

Rhizobium loti (Mesorhizobium loti) [Complete proteome] [HAMAP]

Taxonomic identifier

381 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Phyllobacteriaceae › Mesorhizobium

Protein attributes

Sequence length	357 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. HAMAP MF_00047
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: 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: UniProtKB-KW 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 – 357	357	D-alanine--D-alanine ligase A HAMAP MF_00047		PRO_0000177862
Regions
	Domain	143 – 348	206	ATP-grasp
	Nucleotide binding	171 – 226	56	ATP By similarity
Sites
	Metal binding	302	1	Magnesium or manganese 1 By similarity
	Metal binding	315	1	Magnesium or manganese 1 By similarity
	Metal binding	315	1	Magnesium or manganese 2 By similarity
	Metal binding	317	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q98JS0-1 [UniParc]. Last modified October 1, 2001. Version 1. Checksum: 1C096AE7FCD57C8B	FASTA	357	37,875
	10 20 30 40 50 60 MKEKTRVAIL YGGRSAEHDV SRLSAANVLK AIDRTRYEVV PIAISRDGRW RLQPSSEAGA 70 80 90 100 110 120 DGAGAQVPED GVEVALLPGG KGRLVALTKN GEQPDPVDVV FPVLHGPFGE DGSVQGYAEV 130 140 150 160 170 180 ADVAYVGCGI LASAAAMDKD VAKRLLREAG LAVARSVTVL KGDVGSFQEI AGALGLPFFA 190 200 210 220 230 240 KPARQGSSFG VSKVHDRDGF EQAVETALRY DSKALIEEFV DGREIECSVL ERADGSLTVS 250 260 270 280 290 300 PPGEIIPADK HGFYTYEAKY FDAEGAVVKV PADVPADVVA RTSEMAARAF RALGCEAMAR 310 320 330 340 350 VDFFLRADGS LLVNEVNTLP GFTDISMYAK ALAAAGIGYS KVIDVLIEHA LARHRAR

References

[1]

"Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti." Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S., Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y., Nakayama S. , Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M., Tabata S. DNA Res. 7:331-338(2000) [PubMed: 11214968] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: MAFF303099.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000012 Genomic DNA. Translation: BAB49095.1.
RefSeq	NP_103309.1.
3D structure databases
SMR	Q98JS0. Positions 3-351.
ModBase	Search...
Genome annotation databases
GeneID	1225970.
GenomeReviews	Gene locus mll1812 in contig BA000012_GR.
KEGG	mlo:mll1812.
NMPDR	fig|266835.1.peg.1413.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG427092.
OMA	FTDISMY.
Enzyme and pathway databases
BRENDA	6.3.2.4. 3315.
Family and domain databases
HAMAP	MF_00047. Dala_Dala_lig. [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. IPR016185. PreATP-grasp-like. [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_RHILO

Accession

Primary (citable) accession number: Q98JS0

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	October 1, 2001
Last modified:	February 9, 2010
This is version 48 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)