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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Salmonella dublin (strain CT_02021853)
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 sitei11SubstrateUniRule annotation1
Binding sitei44SubstrateUniRule annotation1
Binding sitei64SubstrateUniRule annotation1
Active sitei73Proton donor/acceptorUniRule annotation1
Binding sitei157SubstrateUniRule annotation1
Sitei159Important for catalytic activityUniRule annotation1
Binding sitei190SubstrateUniRule annotation1
Sitei208Important for catalytic activityUniRule annotation1
Active sitei217Proton 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:SeD_A4334
OrganismiSalmonella dublin (strain CT_02021853)
Taxonomic identifieri439851 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella

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_10000992621 – 274Diaminopimelate epimeraseAdd BLAST274

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi73 ↔ 217

Keywords - PTMi

Disulfide bond

Structurei

3D structure databases

ProteinModelPortaliB5FNU5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni8 – 9Substrate bindingUniRule annotation2
Regioni73 – 75Substrate bindingUniRule annotation3
Regioni208 – 209Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.

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.

B5FNU5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQFSKMHGLG NDFMVVDAVT QNVFFSPELI RRLSDRHLGV GFDQLLVVEP
60 70 80 90 100
PYDPELDFHY RIFNADGSEV SQCGNGARCF ARFVRLKGLT NKRDIRVSTA
110 120 130 140 150
NGRMVLSVTE DELVRVNMGE PNFEPAQVPF RANKAEKTYI MRAAEQTILC
160 170 180 190 200
GVVSMGNPHC VIQVDNVDTA AVETLGPVLE SHERFPERAN IGFMQVVRRE
210 220 230 240 250
HIRLRVYERG AGETRACGSG ACAAVAVGIQ QGLLAEEVRV ELPGGRLDIA
260 270
WKGPGHPLYM TGPAAHIYDG FIHL
Length:274
Mass (Da):30,337
Last modified:October 14, 2008 - v1
Checksum:i2FBB315B7DA12AE9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001144 Genomic DNA. Translation: ACH75293.1.
RefSeqiWP_001160671.1. NC_011205.1.

Genome annotation databases

EnsemblBacteriaiACH75293; ACH75293; SeD_A4334.
KEGGised:SeD_A4334.
PATRICi18496730. VBISalEnt111443_4257.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001144 Genomic DNA. Translation: ACH75293.1.
RefSeqiWP_001160671.1. NC_011205.1.

3D structure databases

ProteinModelPortaliB5FNU5.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACH75293; ACH75293; SeD_A4334.
KEGGised:SeD_A4334.
PATRICi18496730. VBISalEnt111443_4257.

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.

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_SALDC
AccessioniPrimary (citable) accession number: B5FNU5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: October 14, 2008
Last modified: November 2, 2016
This is version 56 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.