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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Prochlorococcus marinus (strain MIT 9313)
Status
Reviewed-Annotation score: -Protein inferred from homologyi

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 sitei72SubstrateUniRule annotation1
Active sitei81Proton donorUniRule annotation1
Binding sitei169SubstrateUniRule annotation1
Sitei171Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei202SubstrateUniRule annotation1
Sitei220Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei229Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciPMAR74547:G1G3N-756-MONOMER
UniPathwayiUPA00034; UER00025

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Alternative name(s):
PLP-independent amino acid racemaseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:PMT_0716
OrganismiProchlorococcus marinus (strain MIT 9313)
Taxonomic identifieri74547 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaSynechococcalesProchloraceaeProchlorococcus
Proteomesi
  • UP000001423 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000777011 – 303Diaminopimelate epimeraseAdd BLAST303

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi74547.PMT0716

Structurei

3D structure databases

ProteinModelPortaliQ7V7M5
SMRiQ7V7M5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni82 – 83Substrate bindingUniRule annotation2
Regioni220 – 221Substrate bindingUniRule annotation2
Regioni230 – 231Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
KOiK01778
OMAiSMCGNGG
OrthoDBiPOG091H01QC

Family and domain databases

HAMAPiMF_00197 DAP_epimerase, 1 hit
InterProiView protein in InterPro
IPR018510 DAP_epimerase_AS
IPR001653 DAP_epimerase_DapF
PANTHERiPTHR31689 PTHR31689, 1 hit
PfamiView protein in Pfam
PF01678 DAP_epimerase, 2 hits
TIGRFAMsiTIGR00652 DapF, 1 hit
PROSITEiView protein in PROSITE
PS01326 DAP_EPIMERASE, 1 hit

Sequencei

Sequence statusi: Complete.

Q7V7M5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLVMLQFSKY QGLGNDFLLI DGREDQLTQQ VINPDPAWVR KICDRHFGIG
60 70 80 90 100
ADGLILALPP RADGDLRMQI FNADGSLAEM CGNGIRCLTR FLADIEGDLC
110 120 130 140 150
VQRWNIETLA GIICPVLQED GQICVDMGTP FLDPESIPTT LTIGSAGLPQ
160 170 180 190 200
GECHLGSTSL HVAAVGMGNP HLIVPVEDLE NIPFENWGQR LEKHHAFPAK
210 220 230 240 250
TNVHFLKIHS PNQLEIRVWE RGSGPTLACG TGACASLVAT CLLGLSDDHA
260 270 280 290 300
EVLLPGGVLQ ISWPGRRGSV FMTGPAEPIF DGVLTPLLSP SHAEVLPQDD

QII
Length:303
Mass (Da):32,747
Last modified:October 1, 2003 - v1
Checksum:i55D2D70E12958C9E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX548175 Genomic DNA Translation: CAE20891.1
RefSeqiWP_011130094.1, NC_005071.1

Genome annotation databases

EnsemblBacteriaiCAE20891; CAE20891; PMT_0716
KEGGipmt:PMT_0716

Similar proteinsi

Entry informationi

Entry nameiDAPF_PROMM
AccessioniPrimary (citable) accession number: Q7V7M5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: October 1, 2003
Last modified: March 28, 2018
This is version 88 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health