D-alanine--D-alanine ligase - Bacillus licheniformis (strain DSM 13 / ATCC 14580)

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Reviewed, UniProtKB/Swiss-Prot Q65N65 (DDL_BACLD)

Last modified February 9, 2010. Version 51. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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:	BLi00543, BL02193

Organism

Bacillus licheniformis (strain DSM 13 / ATCC 14580) [Complete proteome] [HAMAP]

Taxonomic identifier

279010 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

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Protein attributes

Sequence length	361 AA.
Sequence status	Complete.
Protein existence	Inferred from homology.

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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.

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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...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 361

361

D-alanine--D-alanine ligase HAMAP MF_00047

PRO_1000030426

Regions

Domain

140 – 345

206

ATP-grasp

Nucleotide binding

173 – 228

ATP By similarity

Sites

Metal binding

299

Magnesium or manganese 1 By similarity

Metal binding

312

Magnesium or manganese 1 By similarity

Metal binding

312

Magnesium or manganese 2 By similarity

Metal binding

314

Magnesium or manganese 2 By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q65N65-1 [UniParc].

Last modified October 25, 2004. Version 1.
Checksum: DA83B729D1862A9B
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FASTA

361

40,057

        10         20         30         40         50         60 
MKTRLGLVYG GKSAEHNVSL QTALAVTKAL DTEKFDIHPI YITEKGEWVR GPQLTEPVSN 

        70         80         90        100        110        120 
VKMLQFEQTG QTFSPAVLNR DMFPGEADAK EDSIDVVFPL LHGPNGEDGT IQGMLELLNV 

       130        140        150        160        170        180 
PYVGNGVLAS SAGMDKVVMK HLFAQAGLDQ AKYVSFLKKT WSQSKEECYA QVEGELGYPC 

       190        200        210        220        230        240 
FVKPANLGSS VGISKCRSRE ELDQAFELAF QYDRKIVVEE GVIGREIELG VLGNDEPVCS 

       250        260        270        280        290        300 
VAGEIAPKKD FYDYKAKYED GDTDLIIPAS LTEDEYETMR SMAVKAFQAI DGSGLVRADF 

       310        320        330        340        350        360 
FLTNEGRVLI NEVNTMPGFT PFSMFPLLWK QSGVEYAELI EKLVALAIER HEEKQQIKHT 


F

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References

[1]

"The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential."
Veith B., Herzberg C., Steckel S., Feesche J., Maurer K.H., Ehrenreich P., Baeumer S., Henne A., Liesegang H., Merkl R., Ehrenreich A., Gottschalk G.
J. Mol. Microbiol. Biotechnol. 7:204-211(2004) [PubMed: 15383718] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

[2]

"Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species."
Rey M.W., Ramaiya P., Nelson B.A., Brody-Karpin S.D., Zaretsky E.J., Tang M., Lopez de Leon A., Xiang H., Gusti V., Clausen I.G., Olsen P.B., Rasmussen M.D., Andersen J.T., Joergensen P.L., Larsen T.S., Sorokin A., Bolotin A., Lapidus A.

Berka R.M.
Genome Biol. 5:R77.1-R77.12(2004) [PubMed: 15461803] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

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Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000002 Genomic DNA. Translation: AAU22144.1. AE017333 Genomic DNA. Translation: AAU39499.1.
RefSeq	YP_077782.1. YP_090192.1.
3D structure databases
HSSP	HSSP built from PDB template 1IOW based on UniProtKB P07862.
SMR	Q65N65. Positions 2-361.
ModBase	Search...
Protein-protein interaction databases
STRING	Q65N65.
Genome annotation databases
GeneID	3030394. 3099263.
GenomeReviews	Gene locus BLi00543 in contig AE017333_GR. Gene locus BL02193 in contig CP000002_GR.
KEGG	bld:BLi00543. bli:BL02193.
NMPDR	fig\|279010.5.peg.679.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HBG427092.
OMA	FTDISMY.
Enzyme and pathway databases
BioCyc	BLIC279010-1:BLI00543-MONOMER. BLIC279010:BL02193-MONOMER.
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...

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Entry information

Entry name

DDL_BACLD

Accession

Primary (citable) accession number: Q65N65
Secondary accession number(s): Q62YL4

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	October 25, 2004
Last modified:	February 9, 2010
This is version 51 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)

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Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents