Reviewed, UniProtKB/Swiss-Prot A8FA55 (DDL_BACP2)

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:	BPUM_0427

Organism

Bacillus pumilus (strain SAFR-032) [Complete proteome] [HAMAP]

Taxonomic identifier

315750 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	360 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. HAMAP MF_00047
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: 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 – 360	360	D-alanine--D-alanine ligase HAMAP MF_00047		PRO_1000057320
Regions
	Domain	139 – 344	206	ATP-grasp
	Nucleotide binding	172 – 227	56	ATP By similarity
Sites
	Metal binding	298	1	Magnesium or manganese 1 By similarity
	Metal binding	311	1	Magnesium or manganese 1 By similarity
	Metal binding	311	1	Magnesium or manganese 2 By similarity
	Metal binding	313	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	A8FA55-1 [UniParc]. Last modified November 13, 2007. Version 1. Checksum: F436D4B60A45E6AD	FASTA	360	39,946
	10 20 30 40 50 60 MKISLGLIYG GKSAEHNVSL QTALAVTKAL NTEKFDIHPI YITEEGEWLR GEKLTEPVSN 70 80 90 100 110 120 VRMLQFEQNA KTFLPTSLNE SMFPQPTSAD EKIDVVFPLL HGPNGEDGTM QGLLELLNIP 130 140 150 160 170 180 YVGNGVLASA AGMDKVMMKD VFAQAGLAQA KHLSFNKKDY EKATPDSLEQ VEQVLGYPCF 190 200 210 220 230 240 VKPANMGSSV GISKCRSKEE LQTAFDLAFQ YDRRVVVEEG VVGREIEIGV LGNDEPKCSV 250 260 270 280 290 300 VGEIAPKTDF YDYKAKYEDG DTDLIIPASV SEDEYKTIHD MAIKAFKSLD GSGLVRADFF 310 320 330 340 350 360 LTEKGEVLIN EVNTMPGFTP FSMFPLLWKH TGVEYPELIE KLVSLAIERH QEKQTIKTTF

References

[1]

"Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032." Gioia J., Yerrapragada S., Qin X., Jiang H., Igboeli O.C., Muzny D., Dugan-Rocha S., Ding Y., Hawes A., Liu W., Perez L., Kovar C., Dinh H., Lee S., Nazareth L., Blyth P., Holder M., Buhay C. , Tirumalai M.R., Liu Y., Dasgupta I., Bokhetache L., Fujita M., Karouia F., Eswara Moorthy P., Siefert J., Uzman A., Buzumbo P., Verma A., Zwiya H., McWilliams B.D., Olowu A., Clinkenbeard K.D., Newcombe D., Golebiewski L., Petrosino J.F., Nicholson W.L., Fox G.E., Venkateswaran K., Highlander S.K., Weinstock G.M. PLoS ONE 2:E928-E928(2007) [PubMed: 17895969] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000813 Genomic DNA. Translation: ABV61122.1.
RefSeq	YP_001485682.1.
3D structure databases
SMR	A8FA55. Positions 3-360.
ModBase	Search...
Protein-protein interaction databases
STRING	A8FA55.
Genome annotation databases
GeneID	5619654.
GenomeReviews	Gene locus BPUM_0427 in contig CP000813_GR.
KEGG	bpu:BPUM_0427.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HBG427092.
OMA	FTDISMY.
Family and domain databases
HAMAP	MF_00047. Dala_Dala_lig. [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. IPR016185. PreATP-grasp-like. [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_BACP2

Accession

Primary (citable) accession number: A8FA55

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 5, 2008
Last sequence update:	November 13, 2007
Last modified:	February 9, 2010
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)