Reviewed, UniProtKB/Swiss-Prot A7Z1L3 (DDL_BACA2)

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:	RBAM_004900

Organism

Bacillus amyloliquefaciens (strain FZB42) [Complete proteome] [HAMAP]

Taxonomic identifier

326423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	354 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 – 354	354	D-alanine--D-alanine ligase		PRO_0000341058
Regions
	Domain	133 – 338	206	ATP-grasp
	Nucleotide binding	166 – 221	56	ATP By similarity
Sites
	Metal binding	292	1	Magnesium or manganese 1 By similarity
	Metal binding	305	1	Magnesium or manganese 1 By similarity
	Metal binding	305	1	Magnesium or manganese 2 By similarity
	Metal binding	307	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	A7Z1L3-1 [UniParc]. Last modified October 23, 2007. Version 1. Checksum: E55EAFAD7042E84C	FASTA	354	39,216
	10 20 30 40 50 60 MYGGKSAEHN VSLQTALAVT KALNTEKFDI HPIYITEKGE WQRGPLLTEP VSNVKMLQLE 70 80 90 100 110 120 QNGESFALSA LNREMFPEAS PDEKAPIDVV FPLLHGPNGE DGTIQGLLEL LNVPYVGNGV 130 140 150 160 170 180 LASSAGMDKV IMKHLFAQAG LPQAKYAAFL KKDWKQTPDS CLQQVEKELG YPCFVKPANL 190 200 210 220 230 240 GSSVGISKCR NREELEKAFE LAFEYDRKIV VEEGIAGREI EIGVLGNDEP KCSAVGEIAP 250 260 270 280 290 300 KTDFYDYKAK YEDGDTDLMI PAQVTDEQYA EISEMAIKAF KAIDGSGLVR ADFFLTNDGQ 310 320 330 340 350 VLINEVNTMP GFTPFSMFPL LWKEAGVDYS DLIEQLVELA KERHAEKQLI KHTF

References

[1]

"Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42." Chen X.H., Koumoutsi A., Scholz R., Eisenreich A., Schneider K., Heinemeyer I., Morgenstern B., Voss B., Hess W.R., Reva O., Junge H., Voigt B., Jungblut P.R., Vater J., Suessmuth R., Liesegang H., Strittmatter A., Gottschalk G., Borriss R. Nat. Biotechnol. 25:1007-1014(2007) [PubMed: 17704766] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000560 Genomic DNA. Translation: ABS72889.1.
RefSeq	YP_001420120.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	5460378.
GenomeReviews	Gene locus RBAM_004900 in contig CP000560_GR.
KEGG	bay:RBAM_004900.
Organism-specific databases
CMR	Search...
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_BACA2

Accession

Primary (citable) accession number: A7Z1L3

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 10, 2008
Last sequence update:	October 23, 2007
Last modified:	November 25, 2008
This is version 14 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)