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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
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.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 sitei73SubstrateUniRule annotation1
Active sitei82Proton donorUniRule annotation1
Binding sitei172SubstrateUniRule annotation1
Sitei174Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei209SubstrateUniRule annotation1
Sitei227Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei236Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciLPLA220668:G137Z-1858-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:lp_2185
OrganismiLactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
Taxonomic identifieri220668 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
Proteomesi
  • UP000000432 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498451 – 332Diaminopimelate epimeraseAdd BLAST332

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi220668.lp_2185.

Structurei

3D structure databases

ProteinModelPortaliQ88V90.
SMRiQ88V90.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni83 – 84Substrate bindingUniRule annotation2
Regioni227 – 228Substrate bindingUniRule annotation2
Regioni237 – 238Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

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

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.

Q88V90-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVKMIKVHG SGNDFYLLDQ TQFQAPLSDA DLKQLAINIC KRDGAGLYDG
60 70 80 90 100
ADGVLVVDKS EHPQVLGRMR VINADGTEAS MCGNGLRTVA RYLGTQNSQE
110 120 130 140 150
DFRVQTMYAD LKVQAVADFA AHVPAYSVEI SPVTFDAQTL GMHANNDATT
160 170 180 190 200
IINEKIPALS ADLKFSAVAV PNPHLIAFVD HDTLVGPELG RIGEWMNDGK
210 220 230 240 250
NQIFPDGVNV SFVEVLGPNS IFVRTFERGV GFTNACGTAM SASSLMYVLL
260 270 280 290 300
HQESTDFNQE IHVTNPGGMV KTVVHQGADE EYWMELIGNA TFVRIVTLPL
310 320 330
EDALQGDYSP VTATETGEQV AYEDFVANLA KA
Length:332
Mass (Da):35,962
Last modified:June 20, 2003 - v1
Checksum:i1D5FF6C6E05441E0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL935263 Genomic DNA. Translation: CCC79406.1.
RefSeqiWP_003644607.1. NC_004567.2.
YP_004889920.1. NC_004567.2.

Genome annotation databases

EnsemblBacteriaiCCC79406; CCC79406; lp_2185.
GeneIDi1063577.
KEGGilpl:lp_2185.
PATRICifig|220668.9.peg.1847.

Similar proteinsi

Entry informationi

Entry nameiDAPF_LACPL
AccessioniPrimary (citable) accession number: Q88V90
Secondary accession number(s): F9UQB7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 20, 2003
Last sequence update: June 20, 2003
Last modified: August 30, 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