Q98KB6 (DDLB_RHILO) 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:	mll1551

Organism

Rhizobium loti (strain MAFF303099) (Mesorhizobium loti) [Complete proteome] [HAMAP]

Taxonomic identifier

266835 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Phyllobacteriaceae › Mesorhizobium

Protein attributes

Sequence length	308 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 – 308	308	D-alanine--D-alanine ligase B HAMAP MF_00047		PRO_0000177863
Regions
	Domain	102 – 302	201	ATP-grasp
	Nucleotide binding	128 – 183	56	ATP By similarity
Sites
	Metal binding	252	1	Magnesium or manganese 1 By similarity
	Metal binding	269	1	Magnesium or manganese 1 By similarity
	Metal binding	269	1	Magnesium or manganese 2 By similarity
	Metal binding	271	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q98KB6 [UniParc]. Last modified October 1, 2001. Version 1. Checksum: 45B0258B0E9A0E50	FASTA	308	33,179
	10 20 30 40 50 60 MKSKHVAVLL GGFSSERPVS LSSGKACADA LENEGYQVTR VDVGRDVGSV LAELKPDVAF 70 80 90 100 110 120 NALHGPFGED GTIQGILEYL GIPYTHSGVL ASALAMNKEQ AKKIVKTVGV PVAESKVANR 130 140 150 160 170 180 FAIQNKHPMK PPYVIKPVNE GSSFGVVIVS EGQSHPPQVV GSSEWKYGDT VMVERYIHGR 190 200 210 220 230 240 ELTCAVMGDV ALGVCEIIPT GHSFYDYDSK YVAGGSKHEC PAKVSPNIYQ KIQTLALKAH 250 260 270 280 290 300 QAVGCRGVSR SDFRYDDRHS ENGEVVWLEV NTQPGMTPTS LVPEIAAHAG HSFGELLSWM VEDASCLR

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.

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Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000012 Genomic DNA. Translation: BAB48898.1.
RefSeq	NP_103112.1. NC_002678.2.
3D structure databases
ProteinModelPortal	Q98KB6.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1225775.
GenomeReviews	Gene locus mll1551 in contig BA000012_GR.
KEGG	mlo:mll1551.
NMPDR	fig|266835.1.peg.1217.
PATRIC	22476678. VBIMesLot2464_1249.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG427092.
OMA	TDGWYDY.
ProtClustDB	PRK01372.
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_RHILO

Accession

Primary (citable) accession number: Q98KB6

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	October 1, 2001
Last modified:	January 25, 2012
This is version 61 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program