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Q4FP10 (DAPF_PELUB) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 59. 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:SAR11_0257
OrganismPelagibacter ubique (strain HTCC1062) [Complete proteome] [HAMAP]
Taxonomic identifier335992 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaSAR11 clusterCandidatus Pelagibacter

Protein attributes

Sequence length274 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 – 274274Diaminopimelate epimerase HAMAP-Rule MF_00197
PRO_1000011923

Regions

Region10 – 112Substrate binding By similarity
Region72 – 743Substrate binding By similarity
Region209 – 2102Substrate binding By similarity
Region219 – 2202Substrate binding By similarity

Sites

Active site721Proton donor/acceptor By similarity
Active site2181Proton donor/acceptor By similarity
Binding site131Substrate By similarity
Binding site451Substrate By similarity
Binding site631Substrate By similarity
Binding site1581Substrate By similarity
Binding site1911Substrate By similarity
Site1601Important for catalytic activity By similarity
Site2091Important for catalytic activity By similarity

Amino acid modifications

Disulfide bond72 ↔ 218 HAMAP-Rule MF_00197

Sequences

Sequence LengthMass (Da)Tools
Q4FP10 [UniParc].

Last modified August 30, 2005. Version 1.
Checksum: 4DDA04FC3A543FB6

FASTA27430,102
        10         20         30         40         50         60 
MDIKAFKMDG LGNDFVIIDQ RSQDFNLDKD QIIKICDRSF IGCDQLILIK KNKEIDANVE 

        70         80         90        100        110        120 
FFNSDGSISG ACGNGTRCVA DLLSKESGKK EITLLTTSGS LKSKILGNNL VETEIGIPKV 

       130        140        150        160        170        180 
NWQEIPLSKQ LDTQDLKIEI IDRNNTKHIG GIAINVGNPH IIFFVDDIEA FDLKNIGPKI 

       190        200        210        220        230        240 
ENHPLFPEKC NVTLAKVINR NLIKVKVWER GAGLTKACGT AACATAVAAN INNLVEKTTD 

       250        260        270 
IEFVLGSLTI SIDERNSIHM KGPVSDIKNI NIKL 

« Hide

References

[1]"Genome streamlining in a cosmopolitan oceanic bacterium."
Giovannoni S.J., Tripp H.J., Givan S., Podar M., Vergin K.L., Baptista D., Bibbs L., Eads J., Richardson T.H., Noordewier M., Rappe M.S., Short J.M., Carrington J.C., Mathur E.J.
Science 309:1242-1245(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HTCC1062.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000084 Genomic DNA. Translation: AAZ21079.1.
RefSeqYP_265682.1. NC_007205.1.

3D structure databases

ProteinModelPortalQ4FP10.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING335992.SAR11_0257.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAZ21079; AAZ21079; SAR11_0257.
GeneID3517586.
KEGGpub:SAR11_0257.
PATRIC31989971. VBICanPel5618_0256.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0253.
HOGENOMHOG000220466.
KOK01778.
OMAKMRIFNN.
OrthoDBEOG6ND0M5.

Enzyme and pathway databases

BioCycCPEL335992:GH3Z-257-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_PELUB
AccessionPrimary (citable) accession number: Q4FP10
Entry history
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: August 30, 2005
Last modified: June 11, 2014
This is version 59 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