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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Gemmatimonas aurantiaca (strain T-27 / DSM 14586 / JCM 11422 / NBRC 100505)
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 sitei46SubstrateUniRule annotation1
Binding sitei65SubstrateUniRule annotation1
Active sitei74Proton donor/acceptorUniRule annotation1
Sitei148Important for catalytic activityUniRule annotation1
Binding sitei180SubstrateUniRule annotation1
Sitei198Important for catalytic activityUniRule annotation1
Active sitei208Proton 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:GAU_1611
OrganismiGemmatimonas aurantiaca (strain T-27 / DSM 14586 / JCM 11422 / NBRC 100505)
Taxonomic identifieri379066 [NCBI]
Taxonomic lineageiBacteriaGemmatimonadetesGemmatimonadalesGemmatimonadaceaeGemmatimonas
Proteomesi
  • UP000002209 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_10002040611 – 277Diaminopimelate epimeraseAdd BLAST277

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi74 ↔ 208

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi379066.GAU_1611.

Structurei

3D structure databases

ProteinModelPortaliC1A8U3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni74 – 76Substrate bindingUniRule annotation3
Regioni198 – 199Substrate bindingUniRule annotation2
Regioni209 – 210Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107U5Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiNTGSPHY.
OrthoDBiPOG091H01QC.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.

Sequencei

Sequence statusi: Complete.

C1A8U3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFVKMTGSG NDFVFFDGRT TPIDLVTQPE AIKAICNRYN GIGADGLVVL
60 70 80 90 100
EPLQEEADVR VHYYNSDGTA ADLCGNATLC STAISAQWGI TSASGMRLAT
110 120 130 140 150
GAGLINSRID GLPAIALQPI TDIRPDMPIA PATAQGRRVG FAVAGIPHLV
160 170 180 190 200
ILCEDADAVD VAGAGPALRR HEATGPAGAN VNWVSPRPDG SWRYRTFERG
210 220 230 240 250
VEGETLACGT GAVATAVLLR SWGLSDGATT TIRTSSGRDV EVDLEPLTAP
260 270
DGRSLEGFRP TLRGEGRVVF RGEIAGL
Length:277
Mass (Da):28,993
Last modified:May 26, 2009 - v1
Checksum:i729354861C6A19DF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009153 Genomic DNA. Translation: BAH38653.1.

Genome annotation databases

EnsemblBacteriaiBAH38653; BAH38653; GAU_1611.
KEGGigau:GAU_1611.
PATRICi21956116. VBIGemAur55831_1657.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009153 Genomic DNA. Translation: BAH38653.1.

3D structure databases

ProteinModelPortaliC1A8U3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi379066.GAU_1611.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAH38653; BAH38653; GAU_1611.
KEGGigau:GAU_1611.
PATRICi21956116. VBIGemAur55831_1657.

Phylogenomic databases

eggNOGiENOG4107U5Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiNTGSPHY.
OrthoDBiPOG091H01QC.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_GEMAT
AccessioniPrimary (citable) accession number: C1A8U3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: May 26, 2009
Last modified: November 2, 2016
This is version 41 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, Reference 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.