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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Bacteroides fragilis (strain YCH46)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei15SubstrateUniRule annotation1
Binding sitei48SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donor/acceptorUniRule annotation1
Binding sitei150SubstrateUniRule annotation1
Sitei152Important for catalytic activityUniRule annotation1
Binding sitei183SubstrateUniRule annotation1
Sitei201Important for catalytic activityUniRule annotation1
Active sitei210Proton donor/acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:BF2642
OrganismiBacteroides fragilis (strain YCH46)
Taxonomic identifieri295405 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesBacteroidaceaeBacteroides
Proteomesi
  • UP000002197 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000118411 – 269Diaminopimelate epimeraseAdd BLAST269

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi75 ↔ 210

Keywords - PTMi

Disulfide bond

Structurei

3D structure databases

ProteinModelPortaliQ64SY7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni75 – 77Substrate bindingUniRule annotation3
Regioni201 – 202Substrate bindingUniRule annotation2
Regioni211 – 212Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000073580.
KOiK01778.
OMAiNGMRCVV.
OrthoDBiPOG091H01QC.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q64SY7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARAIQFTKM HGTGNDYIYV NTLRFPIARP EKAAIEWSAY HTGIGSDGLV
60 70 80 90 100
LIGHSDKADF SMRIFNADGS EAMMCGNASR CIGKYLYEYG LTSKNVITLD
110 120 130 140 150
TLSGIKILEL HLEGRTVETV TVDMGVPLET DTIDFDGEFP FLSTQVSMGN
160 170 180 190 200
PHLVTFVDDI RIVNLSEMGP KLEKHPLFPD RTNVEFAQIT GENTIRMRVW
210 220 230 240 250
ERGSGITQAC GTGACATAVA AHLTGRTGRT VNVVMDGGTL TIEWDEATGH
260
ISMTGPAVKV FDGTIELRE
Length:269
Mass (Da):29,368
Last modified:October 25, 2004 - v1
Checksum:iDBE82CC62E974EE9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006841 Genomic DNA. Translation: BAD49392.1.
RefSeqiWP_011202959.1. NC_006347.1.
YP_099926.1. NC_006347.1.

Genome annotation databases

EnsemblBacteriaiBAD49392; BAD49392; BF2642.
GeneIDi3083667.
KEGGibfr:BF2642.
PATRICi21050915. VBIBacFra17906_2554.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006841 Genomic DNA. Translation: BAD49392.1.
RefSeqiWP_011202959.1. NC_006347.1.
YP_099926.1. NC_006347.1.

3D structure databases

ProteinModelPortaliQ64SY7.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD49392; BAD49392; BF2642.
GeneIDi3083667.
KEGGibfr:BF2642.
PATRICi21050915. VBIBacFra17906_2554.

Phylogenomic databases

HOGENOMiHOG000073580.
KOiK01778.
OMAiNGMRCVV.
OrthoDBiPOG091H01QC.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_BACFR
AccessioniPrimary (citable) accession number: Q64SY7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: October 25, 2004
Last modified: September 7, 2016
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.