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B3Q862 (DAPF_RHOPT) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 39. 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:Rpal_0251
OrganismRhodopseudomonas palustris (strain TIE-1) [Complete proteome] [HAMAP]
Taxonomic identifier395960 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeRhodopseudomonas

Protein attributes

Sequence length293 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 – 293293Diaminopimelate epimerase HAMAP-Rule MF_00197
PRO_1000099260

Regions

Region14 – 152Substrate binding By similarity
Region76 – 783Substrate binding By similarity
Region215 – 2162Substrate binding By similarity

Sites

Active site761Proton donor/acceptor By similarity
Active site2241Proton donor/acceptor By similarity
Binding site171Substrate By similarity
Binding site471Substrate By similarity
Binding site671Substrate By similarity
Binding site1641Substrate By similarity
Binding site1971Substrate By similarity
Site1661Important for catalytic activity By similarity
Site2151Important for catalytic activity By similarity

Amino acid modifications

Disulfide bond76 ↔ 224 HAMAP-Rule MF_00197

Sequences

Sequence LengthMass (Da)Tools
B3Q862 [UniParc].

Last modified September 2, 2008. Version 1.
Checksum: FE62A4E6E200E122

FASTA29331,904
        10         20         30         40         50         60 
MSALDNRLFA KMNGIGNEIV VVDLRDQPAP VTPADARAVA AHVPYDQLML LQPARLPGTE 

        70         80         90        100        110        120 
AFVRIYNNDG SESGACGNGM RCVARQMFAG SDKNGLTFET RAGLLNCWRG PADGLYTVDM 

       130        140        150        160        170        180 
GEPKFGWQDI PLAEEFRDTR MIELQIGPID APVLHTPSVV SMGNPHAIFW VDDVNAYDLG 

       190        200        210        220        230        240 
RFGPLLENHP IFPERANITL AHIVDRQHIT MRTWERGAGL TKACGSAACA TAVAAARLKR 

       250        260        270        280        290 
TDRTVEMTLP GGQLTIEWRD NDNHVLMTGG AEFEFEGRFD PALFAGALDP TGA 

« Hide

References

[1]"Complete sequence of Rhodopseudomonas palustris TIE-1."
US DOE Joint Genome Institute
Lucas S., Copeland A., 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., Mikhailova N. expand/collapse author list , Emerson D., Newman D.K., Roden E., Richardson P.
Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: TIE-1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001096 Genomic DNA. Translation: ACE98811.1.
RefSeqYP_001989287.1. NC_011004.1.

3D structure databases

ProteinModelPortalB3Q862.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING395960.Rpal_0251.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACE98811; ACE98811; Rpal_0251.
GeneID6407895.
KEGGrpt:Rpal_0251.
PATRIC23304848. VBIRhoPal88240_0256.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0253.
HOGENOMHOG000220466.
KOK01778.
OMALNAVEHE.
OrthoDBEOG6ND0M5.
ProtClustDBPRK00450.

Enzyme and pathway databases

BioCycRPAL395960:GHPC-253-MONOMER.
UniPathwayUPA00034; UER00025.

Family and domain databases

HAMAPMF_00197. DAP_epimerase.
InterProIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERPTHR31689:SF0. PTHR31689:SF0. 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_RHOPT
AccessionPrimary (citable) accession number: B3Q862
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 2, 2008
Last modified: February 19, 2014
This is version 39 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