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C5CND4 (DAPF_VARPS) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 35. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Diaminopimelate epimerase

Short name=DAP epimerase
EC=5.1.1.7
Gene names
Name:dapF
Ordered Locus Names:Vapar_0899
OrganismVariovorax paradoxus (strain S110) [Complete proteome] [HAMAP]
Taxonomic identifier543728 [NCBI]
Taxonomic lineageBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeVariovorax

Protein attributes

Sequence length294 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan By similarity. HAMAP-Rule MF_00197

Catalytic activity

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate. HAMAP-Rule MF_00197

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. HAMAP-Rule MF_00197

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00197.

Sequence similarities

Belongs to the diaminopimelate epimerase family.

Ontologies

Keywords
   Biological processAmino-acid biosynthesis
Lysine biosynthesis
   Cellular componentCytoplasm
   Molecular functionIsomerase
   PTMDisulfide bond
   Technical termComplete proteome
Gene Ontology (GO)
   Biological_processlysine biosynthetic process via diaminopimelate

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functiondiaminopimelate epimerase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 294294Diaminopimelate epimerase HAMAP-Rule MF_00197
PRO_1000204070

Regions

Region78 – 803Substrate binding By similarity
Region224 – 2252Substrate binding By similarity
Region234 – 2352Substrate binding By similarity

Sites

Active site781Proton donor/acceptor By similarity
Active site2331Proton donor/acceptor By similarity
Binding site131Substrate By similarity
Binding site461Substrate By similarity
Binding site691Substrate By similarity
Binding site1731Substrate By similarity
Binding site2061Substrate By similarity
Site1751Important for catalytic activity By similarity
Site2241Important for catalytic activity By similarity

Amino acid modifications

Disulfide bond78 ↔ 233 HAMAP-Rule MF_00197

Sequences

Sequence LengthMass (Da)Tools
C5CND4 [UniParc].

Last modified July 28, 2009. Version 1.
Checksum: 5279A4320AD6A5F4

FASTA29431,618
        10         20         30         40         50         60 
MRIRFTKMQG AGNDFVVLDE TRGTLGLTAA QYRFLADRHF GVGADQILTV RPPSKGAAEG 

        70         80         90        100        110        120 
VDFQYVIHNA DGGEVEQCGN GARCFMRFVR EHHLTDKDTV RVETLAGIIE PRMGADGRVT 

       130        140        150        160        170        180 
VDMGPPIFEP ARVPFDTAGL DPQPTGSWHT WHLALGTHAD SAIVSVAVLS MGNPHAVQVV 

       190        200        210        220        230        240 
DNVDTAPVAR QGPLIEHHPR FAQRVNAGFM QVVDRSHIKL RVFERGAGET LACGTGACAA 

       250        260        270        280        290 
VVAGIRLGLL ERRVDVQTHG GVLTIGWEGE GHPVLMTGPA TTVFEGDIEV PELP 

« Hide

References

[1]"Complete genome sequence of the metabolically versatile plant growth-promoting endophyte, Variovorax paradoxus S110."
Han J.I., Choi H.K., Lee S.W., Orwin P.M., Kim J., Laroe S.L., Kim T.G., O'Neil J., Leadbetter J.R., Lee S.Y., Hur C.G., Spain J.C., Ovchinnikova G., Goodwin L., Han C.
J. Bacteriol. 193:1183-1190(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: S110.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001635 Genomic DNA. Translation: ACS17550.1.
RefSeqYP_002942816.1. NC_012791.1.

3D structure databases

ProteinModelPortalC5CND4.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING543728.Vapar_0899.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACS17550; ACS17550; Vapar_0899.
GeneID7970074.
KEGGvap:Vapar_0899.
PATRIC24002200. VBIVarPar36677_0909.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0253.
HOGENOMHOG000220466.
KOK01778.
OMALIVEPPY.
OrthoDBEOG6ND0M5.

Enzyme and pathway databases

BioCycVPAR543728:GHLL-906-MONOMER.
UniPathwayUPA00034; UER00025.

Family and domain databases

HAMAPMF_00197. DAP_epimerase.
InterProIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERPTHR31689. PTHR31689. 1 hit.
PfamPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsTIGR00652. DapF. 1 hit.
PROSITEPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDAPF_VARPS
AccessionPrimary (citable) accession number: C5CND4
Entry history
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 28, 2009
Last modified: June 11, 2014
This is version 35 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