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A5F4I6 (DAPF_VIBC3) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 50. 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:VC0395_A2393, VC395_0054
OrganismVibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) [Complete proteome] [HAMAP]
Taxonomic identifier345073 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio

Protein attributes

Sequence length276 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.

Sequence caution

The sequence ACP08082.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

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 – 276276Diaminopimelate epimerase HAMAP-Rule MF_00197
PRO_1000071717

Regions

Region10 – 112Substrate binding By similarity
Region75 – 773Substrate binding By similarity
Region210 – 2112Substrate binding By similarity

Sites

Active site751Proton donor/acceptor By similarity
Active site2191Proton donor/acceptor By similarity
Binding site131Substrate By similarity
Binding site461Substrate By similarity
Binding site661Substrate By similarity
Binding site1591Substrate By similarity
Binding site1921Substrate By similarity
Site1611Important for catalytic activity By similarity
Site2101Important for catalytic activity By similarity

Amino acid modifications

Disulfide bond75 ↔ 219 HAMAP-Rule MF_00197

Sequences

Sequence LengthMass (Da)Tools
A5F4I6 [UniParc].

Last modified June 12, 2007. Version 1.
Checksum: 8FCFEC10E5DD714B

FASTA27630,651
        10         20         30         40         50         60 
MHFHFSKMHG LGNDFMVVDC ITQNVFFSPE LIRRLADRHT GVGFDQLLVV EAPYDPESDF 

        70         80         90        100        110        120 
HYRIFNADGS EVEQCGNGAR CFARFVRMKG LTNKYTIHVS TKKGKMVLNV EEEDLITVNM 

       130        140        150        160        170        180 
GVPEFEPNKI PFRAKQSEKT YILRVGEHTL FCGAVSMGNP HVVTVVDDIR TAAVETLGPL 

       190        200        210        220        230        240 
LESHERFPER VNAGFMQVVS RDEINLRVYE RGAGETQACG SGACAAVAVG ILQGLLDEQV 

       250        260        270 
RVHLPGGELE IHWQGPGKPL YMTGPATHIY DGQISC 

« Hide

References

[1]Heidelberg J.
Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 39541 / Classical Ogawa 395 / O395.
[2]"A recalibrated molecular clock and independent origins for the cholera pandemic clones."
Feng L., Reeves P.R., Lan R., Ren Y., Gao C., Zhou Z., Ren Y., Cheng J., Wang W., Wang J., Qian W., Li D., Wang L.
PLoS ONE 3:E4053-E4053(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 39541 / Classical Ogawa 395 / O395.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000627 Genomic DNA. Translation: ABQ19755.1.
CP001235 Genomic DNA. Translation: ACP08082.1. Different initiation.
RefSeqYP_001218293.1. NC_009457.1.
YP_002818318.1. NC_012582.1.

3D structure databases

ProteinModelPortalA5F4I6.
SMRA5F4I6. Positions 4-275.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING345073.VC0395_A2393.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABQ19755; ABQ19755; VC0395_A2393.
ACP08082; ACP08082; VC395_0054.
GeneID5137009.
7776703.
KEGGvco:VC0395_A2393.
vcr:VC395_0054.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0253.
HOGENOMHOG000220466.
KOK01778.
OMACFARFVL.
ProtClustDBPRK00450.

Enzyme and pathway databases

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_VIBC3
AccessionPrimary (citable) accession number: A5F4I6
Secondary accession number(s): C3M2B8
Entry history
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: June 12, 2007
Last modified: April 16, 2014
This is version 50 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