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B1YSS6 (DDL_BURA4) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 44. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended 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:BamMC406_0490
OrganismBurkholderia ambifaria (strain MC40-6) [Complete proteome] [HAMAP]
Taxonomic identifier398577 [NCBI]
Taxonomic lineageBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiaBurkholderia cepacia complex

Protein attributes

Sequence length313 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Cell wall formation By similarity. HAMAP-Rule MF_00047

Catalytic activity

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP-Rule MF_00047

Cofactor

Binds 2 magnesium or manganese ions per subunit By similarity.

Pathway

Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP-Rule MF_00047

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00047.

Sequence similarities

Belongs to the D-alanine--D-alanine ligase family.

Contains 1 ATP-grasp domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 313313D-alanine--D-alanine ligase HAMAP-Rule MF_00047
PRO_1000091164

Regions

Domain108 – 308201ATP-grasp
Nucleotide binding138 – 19356ATP By similarity

Sites

Metal binding2621Magnesium or manganese 1 By similarity
Metal binding2751Magnesium or manganese 1 By similarity
Metal binding2751Magnesium or manganese 2 By similarity
Metal binding2771Magnesium or manganese 2 By similarity

Secondary structure

........................................................ 313
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
B1YSS6 [UniParc].

Last modified May 20, 2008. Version 1.
Checksum: 494D539CF13A281A

FASTA31333,393
        10         20         30         40         50         60 
MSGIDPKRFG KVAVLFGGES AEREVSLTSG RLVLQGLRDA GIDAHPFDPA ERPLSALKDE 

        70         80         90        100        110        120 
GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL GLDKFRTKLV WQQTGVPTPP 

       130        140        150        160        170        180 
FETVMRGDDY AARATDIVAK LGLPLFVKPA SEGSSVAVLK VKTADALPAA LSEAATHDKI 

       190        200        210        220        230        240 
VIVEKSIEGG GEYTACIAGD LDLPLIKIVP AGEFYDYHAK YVANDTQYLI PCGLPAEQET 

       250        260        270        280        290        300 
ELKRIARRAF DVLGCTDWGR ADFMLDAAGN AYFLEVNTAP GMTDHSLPPK AARSIGIGYS 

       310 
ELVVKVLSLT LND 

« Hide

References

[1]"Complete sequence of chromosome 1 of Burkholderia ambifaria MC40-6."
Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Lang D., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A. expand/collapse author list , Ramette A., Konstantinidis K., Tiedje J., Richardson P.
Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: MC40-6.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001025 Genomic DNA. Translation: ACB62987.1.
RefSeqYP_001807203.1. NC_010551.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4EG0X-ray1.65A/B1-313[»]
ProteinModelPortalB1YSS6.
SMRB1YSS6. Positions 10-309.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING398577.BamMC406_0490.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACB62987; ACB62987; BamMC406_0490.
GeneID6177804.
KEGGbac:BamMC406_0490.
PATRIC19030268. VBIBurAmb82852_0485.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG1181.
HOGENOMHOG000011592.
KOK01921.
OMADTQYRIP.
OrthoDBEOG6ND0KB.
ProtClustDBPRK01372.

Enzyme and pathway databases

BioCycBAMB398577:GH38-510-MONOMER.
UniPathwayUPA00219.

Family and domain databases

Gene3D3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPMF_00047. Dala_Dala_lig.
InterProIPR011761. 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.
IPR016185. PreATP-grasp_dom.
[Graphical view]
PANTHERPTHR23132. PTHR23132. 1 hit.
PfamPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 2 hits.
[Graphical view]
SUPFAMSSF52440. SSF52440. 1 hit.
TIGRFAMsTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDDL_BURA4
AccessionPrimary (citable) accession number: B1YSS6
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: May 20, 2008
Last modified: February 19, 2014
This is version 44 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways