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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Pseudomonas entomophila (strain L48)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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.

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.

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.
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 sitei13Substrate1
Binding sitei46Substrate1
Binding sitei66Substrate1
Active sitei75Proton donor1
Binding sitei159Substrate1
Sitei161Could be important to modulate the pK values of the two catalytic cysteine residues1
Binding sitei192Substrate1
Sitei210Could be important to modulate the pK values of the two catalytic cysteine residues1
Active sitei219Proton acceptor1
Sitei270Important for dimerization1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimerase (EC:5.1.1.7)
Short name:
DAP epimerase
Alternative name(s):
PLP-independent amino acid racemase
Gene namesi
Name:dapF
Ordered Locus Names:PSEEN5366
OrganismiPseudomonas entomophila (strain L48)
Taxonomic identifieri384676 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000000658 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119321 – 276Diaminopimelate epimeraseAdd BLAST276

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi384676.PSEEN5366.

Structurei

3D structure databases

ProteinModelPortaliQ1I303.
SMRiQ1I303.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate binding2
Regioni210 – 211Substrate binding2
Regioni220 – 221Substrate binding2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMCGNGGR.
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.

Q1I303-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLLRFTKMHG LGNDFMVLDL VSQHAHIQPK HAKQWGDRNT GIGFDQLLIV
60 70 80 90 100
EAPSNPDVDF RYRIFNADGS EVEQCGNGAR CFARFVLDKR LTAKKRIRVE
110 120 130 140 150
TKGGIIELDV RNDGQVCVDM GPPRFVPADI PFIADEQALS YPLEVDGQVH
160 170 180 190 200
QIAAVSMGNP HSVLRVDDVR TAPVHELGPK IEHHPRFPQR VNAGFIQVVD
210 220 230 240 250
RHRANLRVWE RGAGETQACG TGACAAAVAA IAQGWMDSPV TIDLPGGRLS
260 270
IEWAGPGKPV LMTGPAVRVF EGQVRL
Length:276
Mass (Da):30,303
Last modified:June 13, 2006 - v1
Checksum:i4C7EA23EA7BEDF80
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CT573326 Genomic DNA. Translation: CAK17983.1.
RefSeqiWP_011536341.1. NC_008027.1.

Genome annotation databases

EnsemblBacteriaiCAK17983; CAK17983; PSEEN5366.
GeneIDi32808277.
KEGGipen:PSEEN5366.

Similar proteinsi

Entry informationi

Entry nameiDAPF_PSEE4
AccessioniPrimary (citable) accession number: Q1I303
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: June 13, 2006
Last modified: November 22, 2017
This is version 77 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

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families