Reviewed, UniProtKB/Swiss-Prot Q5WDW9 (DDL_BACSK)

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:	ABC2907

Organism

Bacillus clausii (strain KSM-K16) [Complete proteome] [HAMAP]

Taxonomic identifier

66692 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	368 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 – 368	368	D-alanine--D-alanine ligase		PRO_1000057321
Regions
	Domain	145 – 348	204	ATP-grasp
	Nucleotide binding	175 – 230	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)
	Q5WDW9-1 [UniParc]. Last modified November 23, 2004. Version 1. Checksum: 081C342A37B1F811	FASTA	368	40,081
	10 20 30 40 50 60 MAKKRVGIIF GGKSAEHEVS LQSAKNIVEA IDKDRFDVTL IGIDKQGQWH INEASNFLLN 70 80 90 100 110 120 ADNPALIELN KSNQGVALIP GKEDRQLVGT ANQSVLDQLD VVFPIVHGTL GEDGSLQGMF 130 140 150 160 170 180 RLANLPFVGS NVLGSAVSMD KDIAKRLLQG AGLHVASGLT FTRAAKETID FESIADQLGL 190 200 210 220 230 240 PLFIKPANQG SSVGVNKATT EAEFTAAIEE AFSYDHKVLI EAAIKGREIE CAVLGNDYPK 250 260 270 280 290 300 ASTCGEILPQ DGFYSYDAKY IDEDGAKLAI PADLPEDVNR RIQDIAIQAY KTLNCEGLAR 310 320 330 340 350 360 VDVFLTETGE VIINEVNTLP GFTKISMYPK LWEASGVSYQ DLITTLIELA IERHERDKQL KSSVFDRN

References

[1]	"The complete genome sequence of the alkaliphilic Bacillus clausii KSM-K16." Takaki Y., Kageyama Y., Shimamura S., Suzuki H., Nishi S., Hatada Y., Kawai S., Ito S., Horikoshi K. Submitted (OCT-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AP006627 Genomic DNA. Translation: BAD65441.1.
RefSeq	YP_176402.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	3203892.
GenomeReviews	Gene locus ABC2907 in contig AP006627_GR.
KEGG	bcl:ABC2907.
NMPDR	fig|66692.3.peg.2796.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q5WDW9.
Enzyme and pathway databases
BioCyc	BCLA66692:ABC2907-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_BACSK

Accession

Primary (citable) accession number: Q5WDW9

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 5, 2008
Last sequence update:	November 23, 2004
Last modified:	November 25, 2008
This is version 36 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)