D-alanine--D-alanine ligase - Agrobacterium tumefaciens (strain C58 / ATCC 33970)

Contribute

Send feedback

Read comments (?) or add your own

Q8UDN3 (DDL_AGRT5) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 69. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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
Ordered Locus Names:	Atu2089
ORF Names:	AGR_C_3788

Organism

Agrobacterium tumefaciens (strain C58 / ATCC 33970)

Taxonomic identifier

176299 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Rhizobiaceae › Rhizobium/Agrobacterium group › Agrobacterium

Protein attributes

Sequence length	308 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 – 308

308

D-alanine--D-alanine ligase HAMAP MF_00047

PRO_0000177777

Regions

Domain

102 – 302

201

ATP-grasp

Nucleotide binding

128 – 183

ATP By similarity

Sites

Metal binding

252

Magnesium or manganese 1 By similarity

Metal binding

269

Magnesium or manganese 1 By similarity

Metal binding

269

Magnesium or manganese 2 By similarity

Metal binding

271

Magnesium or manganese 2 By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q8UDN3 [UniParc].

Last modified August 2, 2002. Version 2.
Checksum: 18A95347199404E8
Show »

FASTA

308

33,069

        10         20         30         40         50         60 
MGGKHVAVLL GGFSSERPVS LSSGNACALA LEGEGYKVTR VDVGRDVAAV LDELRPDVAF 

        70         80         90        100        110        120 
NALHGPFGED GTIQGILEYL AIPYTHSGVL ASALAMDKAQ AKKVAAAAGI PVAGERVMNR 

       130        140        150        160        170        180 
FDFTSEHPLQ PPYVVKPVRE GSSFGVVIVK EDQSHPPQIL TSSEWPFGNQ VMVERYIHGR 

       190        200        210        220        230        240 
ELTCGVLDGE ALGVTEVVPL GHNFYDYDAK YAAGGSKHVI PAGISPKIYQ KIQTLAVMAH 

       250        260        270        280        290        300 
QAIGCRGVSR SDFRYDDRFS EDGEVIWLEV NTQPGMTPTS LVPEMAAHAG RSFGDLVSWM 


VEDASCLR

« Hide

References

[1]	"The genome of the natural genetic engineer Agrobacterium tumefaciens C58." Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K., Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y., Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P., Clendenning J. Nester E.W. Science 294:2317-2323(2001) [PubMed: 11743193] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C58 / ATCC 33970.
[2]	"Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58." Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B., Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K., Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C. Slater S. Science 294:2323-2328(2001) [PubMed: 11743194] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C58 / ATCC 33970.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE007869 Genomic DNA. Translation: AAK87839.2.
PIR	AB2833. F97610.
RefSeq	NP_355054.2. NC_003062.2.
3D structure databases
ProteinModelPortal	Q8UDN3.
ModBase	Search...
Protein-protein interaction databases
STRING	Q8UDN3.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1134127.
GenomeReviews	Gene locus Atu2089 in contig AE007869_GR.
KEGG	atu:Atu2089.
PATRIC	20813963. VBIAgrTum91616_2102.
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HBG427092.
OMA	TDGWYDY.
PhylomeDB	Q8UDN3.
ProtClustDB	PRK01372.
Enzyme and pathway databases
BioCyc	ATUM176299-1:ATU2089-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. 2 hits. 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. 2 hits. [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_AGRT5

Accession

Primary (citable) accession number: Q8UDN3

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 2, 2002
Last sequence update:	August 2, 2002
Last modified:	January 25, 2012
This is version 69 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

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

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents