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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Pseudomonas putida (strain GB-1)
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

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciPPUT76869:G1GAZ-5434-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:PputGB1_5289
OrganismiPseudomonas putida (strain GB-1)
Taxonomic identifieri76869 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002157 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000777021 – 276Diaminopimelate epimeraseAdd BLAST276

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi76869.PputGB1_5289

Structurei

3D structure databases

ProteinModelPortaliB0KQ41
SMRiB0KQ41
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
KOiK01778
OMAiSMCGNGG

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.

B0KQ41-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLLRFTKMHG LGNDFMVLDL VSQHAHIQPK HAKQWGDRHT GIGFDQLLIV
60 70 80 90 100
EAPNNPEVDF RYRIFNADGS EVEQCGNGAR CFARFVLDKR LTAKKRIRVE
110 120 130 140 150
TKSGIIVLDV QNDGQVSVDM GPPRFIPAEI PFVADAQALS YPLEVDGQLH
160 170 180 190 200
SIAAVSMGNP HAVLRVDDVR TAPVHELGPK IENHPRFPQR VNAGFIQVID
210 220 230 240 250
RHRANLRVWE RGAGETQACG TGACAAAVAA ISQGWMDSPV SLDLPGGRLH
260 270
IEWAGPGKPV LMTGPAVRVY EGQVRL
Length:276
Mass (Da):30,295
Last modified:March 18, 2008 - v1
Checksum:i7D2DF72014E5F4BA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000926 Genomic DNA Translation: ABZ01171.1
RefSeqiWP_012274780.1, NC_010322.1

Genome annotation databases

EnsemblBacteriaiABZ01171; ABZ01171; PputGB1_5289
KEGGippg:PputGB1_5289

Similar proteinsi

Entry informationi

Entry nameiDAPF_PSEPG
AccessioniPrimary (citable) accession number: B0KQ41
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: March 18, 2008
Last modified: March 28, 2018
This is version 61 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

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