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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831)
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 sitei13SubstrateUniRule annotation1
Binding sitei48SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donor/acceptorUniRule annotation1
Binding sitei165SubstrateUniRule annotation1
Sitei167Important for catalytic activityUniRule annotation1
Binding sitei198SubstrateUniRule annotation1
Sitei216Important for catalytic activityUniRule annotation1
Active sitei225Proton 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:OB2354
OrganismiOceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831)
Taxonomic identifieri221109 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeOceanobacillus
Proteomesi
  • UP000000822 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_00001498571 – 286Diaminopimelate epimeraseAdd BLAST286

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi75 ↔ 225

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi221109.OB2354.

Structurei

3D structure databases

ProteinModelPortaliQ8ENX2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni10 – 11Substrate bindingUniRule annotation2
Regioni75 – 77Substrate bindingUniRule annotation3
Regioni216 – 217Substrate bindingUniRule annotation2
Regioni226 – 227Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.
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.

Q8ENX2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIPFTKMHG LGNNYVYIDL FDYAIDEKLY HDLAIQISDV YTGIGSDGMI
60 70 80 90 100
LIHPTTDADV GMRIFNKDGS EGKSCGNGLR CTAKYAYENG IVTNKKFHIQ
110 120 130 140 150
TKANIVEAEV SVDNNKVNQV TIDMGEPILA RNEIPMMGNN DVKVVNEPFV
160 170 180 190 200
VAGETQYITA VSMGNPHGVF FVDDIEKAPL ETLGPTIEKD MRFPESINVE
210 220 230 240 250
FIEVVSPTEL NFRVWERGSG ITQACGTGAC AAVVAATLNE KVTKSHPIVV
260 270 280
HLAGGDLNIE WKEDNHVWMT GPAEVIATGL FYYKEE
Length:286
Mass (Da):31,495
Last modified:March 1, 2003 - v1
Checksum:i45B336210C99D73F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000028 Genomic DNA. Translation: BAC14310.1.
RefSeqiWP_011066745.1. NC_004193.1.

Genome annotation databases

EnsemblBacteriaiBAC14310; BAC14310; BAC14310.
KEGGioih:OB2354.
PATRICi22795760. VBIOceIhe82024_2385.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000028 Genomic DNA. Translation: BAC14310.1.
RefSeqiWP_011066745.1. NC_004193.1.

3D structure databases

ProteinModelPortaliQ8ENX2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi221109.OB2354.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC14310; BAC14310; BAC14310.
KEGGioih:OB2354.
PATRICi22795760. VBIOceIhe82024_2385.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.
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_OCEIH
AccessioniPrimary (citable) accession number: Q8ENX2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 11, 2003
Last sequence update: March 1, 2003
Last modified: November 30, 2016
This is version 87 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.