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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
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 sitei13SubstrateUniRule annotation1
Binding sitei46SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donorUniRule annotation1
Binding sitei159SubstrateUniRule annotation1
Sitei161Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei192SubstrateUniRule annotation1
Sitei210Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei219Proton acceptorUniRule annotation1
Sitei270Important for dimerizationUniRule annotation1

GO - Molecular functioni

  • diaminopimelate epimerase activity Source: PseudoCAP

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciPAER208964:G1FZ6-5399-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:PA5278
OrganismiPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002438 Componenti: Chromosome

Organism-specific databases

PseudoCAPiPA5278

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498591 – 276Diaminopimelate epimeraseAdd BLAST276

Proteomic databases

PaxDbiQ51564

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi208964.PA5278

Structurei

3D structure databases

ProteinModelPortaliQ51564
SMRiQ51564
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate bindingUniRule annotation2
Regioni210 – 211Substrate bindingUniRule annotation2
Regioni220 – 221Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
HOGENOMiHOG000220466
InParanoidiQ51564
KOiK01778
OMAiSMCGNGG
PhylomeDBiQ51564

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.

Q51564-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLLRFTKMHG LGNDFMVLDL VSQHAHVQPK HVKLWGDRNT GIGFDQLLIV
60 70 80 90 100
EAPSSPDVDF RYRIFNADGS EVEQCGNGAR CFARFVQDKR LTVKKSIRVE
110 120 130 140 150
TKGGIIELNI RPDGQVTVDM GPPRLAPAEI PFQAEREALS YEIEVNGQRV
160 170 180 190 200
ELAAVSMGNP HGVLRVENVD SAPVHSLGPQ LEVHPRFPKK ANIGFLQVLD
210 220 230 240 250
PHHARLRVWE RGVGETQACG TGACAAAVAG IRQGWLQSPV QIDLPGGRLH
260 270
IEWAGPGQPV MMTGPAVRVY EGQVRL
Length:276
Mass (Da):30,320
Last modified:December 8, 2000 - v2
Checksum:i42833EEE0611621F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004091 Genomic DNA Translation: AAG08663.1
X78478 Genomic DNA Translation: CAA55224.1
PIRiG82986
S61400 S43154
RefSeqiNP_253965.1, NC_002516.2
WP_003114344.1, NC_002516.2

Genome annotation databases

EnsemblBacteriaiAAG08663; AAG08663; PA5278
GeneIDi877750
KEGGipae:PA5278
PATRICifig|208964.12.peg.5532

Similar proteinsi

Entry informationi

Entry nameiDAPF_PSEAE
AccessioniPrimary (citable) accession number: Q51564
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: December 8, 2000
Last modified: May 23, 2018
This is version 105 of the entry and version 2 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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