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A1VST4 (DDL_POLNA) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 56. 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:Pnap_3415
OrganismPolaromonas naphthalenivorans (strain CJ2) [Complete proteome] [HAMAP]
Taxonomic identifier365044 [NCBI]
Taxonomic lineageBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaePolaromonas

Protein attributes

Sequence length325 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 annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 325325D-alanine--D-alanine ligase HAMAP-Rule MF_00047
PRO_0000341150

Regions

Domain107 – 311205ATP-grasp
Nucleotide binding137 – 19256ATP By similarity

Sites

Metal binding2641Magnesium or manganese 1 By similarity
Metal binding2781Magnesium or manganese 1 By similarity
Metal binding2781Magnesium or manganese 2 By similarity
Metal binding2801Magnesium or manganese 2 By similarity

Sequences

Sequence LengthMass (Da)Tools
A1VST4 [UniParc].

Last modified February 6, 2007. Version 1.
Checksum: A75A4DD1D3D691F3

FASTA32534,584
        10         20         30         40         50         60 
MSPNPSSFGK VAVLMGGRSA EREISLMSGS GVVQALRSQG IDAHAFDPAE RDLGELKTGG 

        70         80         90        100        110        120 
FARCFIALHG RFGEDGTVQG ALELLGIPYT GSGVMASSMA IDKVMTKRLL LSESLPTPRY 

       130        140        150        160        170        180 
VLLRRGGYSP AQVDAIVDTL GLPLIVKPAR EGSSLGLSKV TERAAMAAAV ALAEKMDADI 

       190        200        210        220        230        240 
LCEQFISGDE VTCPVLGTGE QARALPVIRI VAPEGNYDYQ NKYFTDTTQY LVPCGLPAGE 

       250        260        270        280        290        300 
EAAIQQLVLQ AFRTLNCRGW ARADVMIDQA TRKPYLLEIN TSPGMTGHSL VPMSARAAGI 

       310        320 
SYEALCVEVL KTALLDHQPR DGSLP 

« Hide

References

[1]"Complete sequence of chromosome 1 of Polaromonas naphthalenivorans CJ2."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D.R., Brettin T., Bruce D., Han C., Tapia R., Brainard J., Schmutz J. expand/collapse author list , Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Madsen E.L., Richardson P.
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CJ2.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000529 Genomic DNA. Translation: ABM38712.1.
RefSeqYP_983633.1. NC_008781.1.

3D structure databases

ProteinModelPortalA1VST4.
SMRA1VST4. Positions 9-313.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING365044.Pnap_3415.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABM38712; ABM38712; Pnap_3415.
GeneID4688839.
KEGGpna:Pnap_3415.
PATRIC22951551. VBIPolNap76733_4296.

Organism-specific databases

CMRSearch...

Phylogenomic databases

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

Enzyme and pathway databases

BioCycPNAP365044:GJ8X-3464-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_POLNA
AccessionPrimary (citable) accession number: A1VST4
Entry history
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: February 6, 2007
Last modified: February 19, 2014
This is version 56 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

PATHWAY comments

Index of metabolic and biosynthesis pathways