Reviewed, UniProtKB/Swiss-Prot Q65N65 (DDL_BACLD)

Names and origin

Protein names

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

Gene names

Name:	ddl
Ordered Locus Names:	BLi00543, BL02193

Organism

Bacillus licheniformis (strain DSM 13 / ATCC 14580) [Complete proteome] [HAMAP]

Taxonomic identifier

279010 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	361 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 – 361	361	D-alanine--D-alanine ligase		PRO_1000030426
Regions
	Domain	140 – 345	206	ATP-grasp
	Nucleotide binding	173 – 228	56	ATP By similarity
Sites
	Metal binding	299	1	Magnesium or manganese 1 By similarity
	Metal binding	312	1	Magnesium or manganese 1 By similarity
	Metal binding	312	1	Magnesium or manganese 2 By similarity
	Metal binding	314	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q65N65-1 [UniParc]. Last modified October 25, 2004. Version 1. Checksum: DA83B729D1862A9B	FASTA	361	40,057
	10 20 30 40 50 60 MKTRLGLVYG GKSAEHNVSL QTALAVTKAL DTEKFDIHPI YITEKGEWVR GPQLTEPVSN 70 80 90 100 110 120 VKMLQFEQTG QTFSPAVLNR DMFPGEADAK EDSIDVVFPL LHGPNGEDGT IQGMLELLNV 130 140 150 160 170 180 PYVGNGVLAS SAGMDKVVMK HLFAQAGLDQ AKYVSFLKKT WSQSKEECYA QVEGELGYPC 190 200 210 220 230 240 FVKPANLGSS VGISKCRSRE ELDQAFELAF QYDRKIVVEE GVIGREIELG VLGNDEPVCS 250 260 270 280 290 300 VAGEIAPKKD FYDYKAKYED GDTDLIIPAS LTEDEYETMR SMAVKAFQAI DGSGLVRADF 310 320 330 340 350 360 FLTNEGRVLI NEVNTMPGFT PFSMFPLLWK QSGVEYAELI EKLVALAIER HEEKQQIKHT F

References

[1]

"The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential." Veith B., Herzberg C., Steckel S., Feesche J., Maurer K.H., Ehrenreich P., Baeumer S., Henne A., Liesegang H., Merkl R., Ehrenreich A., Gottschalk G. J. Mol. Microbiol. Biotechnol. 7:204-211(2004) [PubMed: 15383718] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

[2]

"Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species." Rey M.W., Ramaiya P., Nelson B.A., Brody-Karpin S.D., Zaretsky E.J., Tang M., Lopez de Leon A., Xiang H., Gusti V., Clausen I.G., Olsen P.B., Rasmussen M.D., Andersen J.T., Joergensen P.L., Larsen T.S., Sorokin A., Bolotin A., Lapidus A. , Galleron N., Ehrlich S.D., Berka R.M. Genome Biol. 5:RESEARCH077.1-RESEARCH077.12(2004) [PubMed: 15461803] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000002 Genomic DNA. Translation: AAU22144.1. AE017333 Genomic DNA. Translation: AAU39499.1.
RefSeq	YP_077782.1. YP_090192.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	3030394. 3099263.
GenomeReviews	Gene locus BL02193 in contig CP000002_GR. Gene locus BLi00543 in contig AE017333_GR.
KEGG	bld:BLi00543. bli:BL02193.
NMPDR	fig|279010.5.peg.679.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q65N65.
Enzyme and pathway databases
BioCyc	BLIC279010:BL02193-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

DDL_BACLD

Accession

Primary (citable) accession number: Q65N65
Secondary accession number(s): Q62YL4

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	October 25, 2004
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)