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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
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 sitei20SubstrateUniRule annotation1
Binding sitei53SubstrateUniRule annotation1
Binding sitei73SubstrateUniRule annotation1
Active sitei82Proton donorUniRule annotation1
Binding sitei167SubstrateUniRule annotation1
Sitei169Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei200SubstrateUniRule annotation1
Sitei218Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei227Proton acceptorUniRule annotation1
Sitei278Important for dimerizationUniRule annotation1

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 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:XOO3767
OrganismiXanthomonas oryzae pv. oryzae (strain MAFF 311018)
Taxonomic identifieri342109 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119851 – 284Diaminopimelate epimeraseAdd BLAST284

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliQ2NYV5
SMRiQ2NYV5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni83 – 84Substrate bindingUniRule annotation2
Regioni218 – 219Substrate bindingUniRule annotation2
Regioni228 – 229Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000165071
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.

Q2NYV5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSADGRSGRL RFTKMHGAGN DFVVLDLRDG TPPPDAALAA QLADRHFGVG
60 70 80 90 100
CDQILTIEAP RSEGAVAAYG IWNSDGSAAR QCGNGARCVA AWLVRDGIAQ
110 120 130 140 150
CERFIIDSPV TAHAVERLEG GRYAVAMGMP QFDPPQIPLA GFAHARDEYA
160 170 180 190 200
LPVHGDTVRF GAVSMGNPHA VVEVGRVDAA PVERVGTLLQ QNAAFPDSVN
210 220 230 240 250
VGFVQVVDPT HVRLRVFERG VGETLACGSG ACAAAVVLMQ RCRVERDVQV
260 270 280
SLPGGELRIR WPCDHEQVVM SGPAVFVFDG EWNG
Length:284
Mass (Da):30,238
Last modified:February 7, 2006 - v1
Checksum:iC0DEF48B1A4D4D66
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008229 Genomic DNA Translation: BAE70522.1
RefSeqiWP_011260363.1, NC_007705.1

Genome annotation databases

EnsemblBacteriaiBAE70522; BAE70522; BAE70522
GeneIDi34180699
KEGGixom:XOO3767

Similar proteinsi

Entry informationi

Entry nameiDAPF_XANOM
AccessioniPrimary (citable) accession number: Q2NYV5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: February 7, 2006
Last modified: March 28, 2018
This is version 76 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health