P96612 (DDL_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-alanine--D-alanine ligase
EC=6.3.2.4

Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase

Gene names

Name:	ddl
Synonyms:	ddlA
Ordered Locus Names:	BSU04560

Organism

Bacillus subtilis

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	354 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.
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 Reference 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: UniProtKB-KW 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: EC metal 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 HAMAP MF_00047		PRO_0000177785
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)
	P96612 [UniParc]. Last modified May 1, 1997. Version 1. Checksum: 889A5D3DECF7F76B	FASTA	354	39,131
	10 20 30 40 50 60 MYGGKSAEHN VSLQTALAVI KALNTEKFDI HPIYITEKGE WVRGARLTEP VSNVKMLQFE 70 80 90 100 110 120 QGGSAFSPAA LNQEMFPQEA SQQNEAIDVV FPLLHGPNGE DGTIQGMLEL LNIPYVGNGV 130 140 150 160 170 180 LASSAGMDKV VMKHLFAQVG LAQAKYAAFL KKDWTRSPKE SCEEVEQELG YPCFVKPANL 190 200 210 220 230 240 GSSVGISKCR NREELQKAFE LAFQYDRKVV VEEGINGREI EIGVLGNDDP KCSVVGEIAP 250 260 270 280 290 300 KTDFYDYKAK YEDGDTDLMI PAIVTDEEYA TISDMAIKAF KAIDGSGLVR ADFFLTADGE 310 320 330 340 350 VLINEVNTMP GFTPFSMFPL LWKEAGVEYA DLIEQLVELA KERHAEKQLI KHTF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A 148 kbp sequence of the region between 35 and 47 degree of the Bacillus subtilis genome." Kasahara Y., Nakai S., Lee S., Sadaie Y., Ogasawara N. Submitted (MAR-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168.
[2]	"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis." Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A. Nature 390:249-256(1997) [PubMed: 9384377] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB001488 Genomic DNA. Translation: BAA19293.1. AL009126 Genomic DNA. Translation: CAB12263.1.
PIR	D69613.
RefSeq	NP_388337.1. NC_000964.3.
3D structure databases
ProteinModelPortal	P96612.
SMR	P96612. Positions 1-354.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	EBBACT00000000837; EBBACP00000000837; EBBACG00000000835.
GeneID	938224.
GenomeReviews	Gene locus BSU04560 in contig AL009126_GR.
KEGG	bsu:BSU04560.
NMPDR	fig|224308.1.peg.456.
PATRIC	18972496. VBIBacSub10457_0476.
Organism-specific databases
GenoList	BSU04560. [Micado]
Phylogenomic databases
GeneTree	EBGT00050000001406.
HOGENOM	HBG427092.
OMA	LLHGPFG.
PhylomeDB	P96612.
ProtClustDB	PRK01966.
Enzyme and pathway databases
BioCyc	BSUB:BSU04560-MONOMER.
Family and domain databases
HAMAP	MF_00047. Dala_Dala_lig. [Tree]
InterPro	IPR011761. ATP-grasp. IPR013815. ATP_grasp_subdomain_1. 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:3.30.1490.20. ATP_grasp_subdomain_1. 1 hit. G3DSA:3.30.470.20. ATP_grasp_subdomain_2. 1 hit. G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.
KO	K01921.
PANTHER	PTHR23132. PTHR23132. 1 hit.
Pfam	PF07478. Dala_Dala_lig_C. 1 hit. PF01820. Dala_Dala_lig_N. 1 hit. [Graphical view]
SUPFAM	SSF52440. PreATP-grasp-like. 1 hit.
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_BACSU

Accession

Primary (citable) accession number: P96612

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	May 1, 1997
Last modified:	January 25, 2012
This is version 91 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program