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Q163J4 (DDL_ROSDO) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 61. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | 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:RD1_3351
OrganismRoseobacter denitrificans (strain ATCC 33942 / OCh 114) (Erythrobacter sp. (strain OCh 114)) (Roseobacter denitrificans) [Complete proteome] [HAMAP]
Taxonomic identifier375451 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRoseobacter

Protein attributes

Sequence length319 AA.
Sequence statusComplete.
Protein existenceInferred from homology

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 caution

The sequence ABG32849.1 differs from that shown. Reason: Erroneous initiation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 319319D-alanine--D-alanine ligase HAMAP-Rule MF_00047
PRO_0000341170

Regions

Domain120 – 313194ATP-grasp
Nucleotide binding147 – 19751ATP By similarity

Sites

Metal binding2641Magnesium or manganese 1 By similarity
Metal binding2801Magnesium or manganese 1 By similarity
Metal binding2801Magnesium or manganese 2 By similarity
Metal binding2821Magnesium or manganese 2 By similarity

Sequences

Sequence LengthMass (Da)Tools
Q163J4 [UniParc].

Last modified June 10, 2008. Version 2.
Checksum: 44CB158B7DB87894

FASTA31933,854
        10         20         30         40         50         60 
MTGPEWAHTR GTKVGQSSRT PPKVAVLLGG PSVEREVSLS SGQACAAALR DEGYDVVEID 

        70         80         90        100        110        120 
AGHDLGARLI DAGPDAVLNC LHGRWGEDGC VQGLLEWMGV PYSHSGVLAS ALAMDKQRSK 

       130        140        150        160        170        180 
DAFVAAGLPV VPSVIAKAAD VRMGHVMQPP YVVKPNNEGS SVGVYLVHEA ANGPPQLSED 

       190        200        210        220        230        240 
MPQEVMVEAF APGRELTTTV VGDRALTVTD IVTDGWYDYD AKYKPGGSHH VVPADIPADI 

       250        260        270        280        290        300 
FDLCMDYALR AHHALGCRGV SRTDFRWDET KGAAGLILLE TNTQPGMTAT SLTPEQAAVT 

       310 
GMTFGKLCAW MVEDASCDR 

« Hide

References

[1]"The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism."
Swingley W.D., Sadekar S., Mastrian S.D., Matthies H.J., Hao J., Ramos H., Acharya C.R., Conrad A.L., Taylor H.L., Dejesa L.C., Shah M.K., O'Huallachain M.E., Lince M.T., Blankenship R.E., Beatty J.T., Touchman J.W.
J. Bacteriol. 189:683-690(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 33942 / OCh 114.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000362 Genomic DNA. Translation: ABG32849.1. Different initiation.
RefSeqYP_683535.1. NC_008209.1.

3D structure databases

ProteinModelPortalQ163J4.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING375451.RD1_3351.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABG32849; ABG32849; RD1_3351.
GeneID4195054.
KEGGrde:RD1_3351.
PATRIC23364663. VBIRosDen86677_3201.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG1181.
HOGENOMHOG000011592.
KOK01921.
OrthoDBEOG6ND0KB.
ProtClustDBPRK01372.

Enzyme and pathway databases

BioCycRDEN375451:GJIZ-3159-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_ROSDO
AccessionPrimary (citable) accession number: Q163J4
Entry history
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: June 10, 2008
Last modified: February 19, 2014
This is version 61 of the entry and version 2 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

PATHWAY comments

Index of metabolic and biosynthesis pathways