Reviewed, UniProtKB/Swiss-Prot A1WC04 (DDL_ACISJ)

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:	Ajs_3668

Organism

Acidovorax sp. (strain JS42) [Complete proteome] [HAMAP]

Taxonomic identifier

232721 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Comamonadaceae › Acidovorax

Protein attributes

Sequence length	332 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. 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.
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	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 – 332	332	D-alanine--D-alanine ligase HAMAP MF_00047		PRO_0000341045
Regions
	Domain	112 – 312	201	ATP-grasp
	Nucleotide binding	138 – 193	56	ATP By similarity
Sites
	Metal binding	265	1	Magnesium or manganese 1 By similarity
	Metal binding	279	1	Magnesium or manganese 1 By similarity
	Metal binding	279	1	Magnesium or manganese 2 By similarity
	Metal binding	281	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1WC04-1 [UniParc]. Last modified February 6, 2007. Version 1. Checksum: 654FFE07031D2598	FASTA	332	35,626
	10 20 30 40 50 60 MSQNDLKIDV KALGKVAVLM GGTSAEREVS LMSGGGVLQA LRSRGVDAHA FDPAHSDLSE 70 80 90 100 110 120 LKAHGYSRCF IALHGRHGED GTVQGALELL GIPYTGPGVM ASSIAMDKIM TKRIWRADGL 130 140 150 160 170 180 PTPDWRLVSS SAETAQAFQE LGAPMIVKPS REGSTIGLTK VTSLGQCEQA YRLAAQHDPE 190 200 210 220 230 240 VLCEQFIDGD ETTCPILGQG TEARALPVIR IEAPQGNYDY QNKYFTDVTQ YHCPSGLPEA 250 260 270 280 290 300 EEREIQRIVV QAYRTLGCRG WARADIMIRA SDRKPFLLEI NTSPGMTGHS LVPMSANASG 310 320 330 ISYPDLCLRI LASASLDALQ GRAGAAGGRE SV

References

[1]

"Complete sequence of chromosome 1 of Acidovorax sp. JS42." Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chertkov O., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M. , Hauser L., Kyrpides N., Kim E., Stahl D., Richardson P. Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000539 Genomic DNA. Translation: ABM43779.1.
RefSeq	YP_987855.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	4673646.
GenomeReviews	Gene locus Ajs_3668 in contig CP000539_GR.
KEGG	ajs:Ajs_3668.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	A1WC04. IEEWLSG.
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_ACISJ

Accession

Primary (citable) accession number: A1WC04

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 10, 2008
Last sequence update:	February 6, 2007
Last modified:	June 16, 2009
This is version 23 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)