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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Shewanella sp. (strain W3-18-1)
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 sitei12SubstrateUniRule annotation1
Binding sitei45SubstrateUniRule annotation1
Binding sitei65SubstrateUniRule annotation1
Active sitei74Proton donorUniRule annotation1
Binding sitei158SubstrateUniRule annotation1
Sitei160Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei191SubstrateUniRule annotation1
Sitei209Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei218Proton acceptorUniRule annotation1
Sitei269Important 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:Sputw3181_3721
OrganismiShewanella sp. (strain W3-18-1)
Taxonomic identifieri351745 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119691 – 275Diaminopimelate epimeraseAdd BLAST275

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliA1RPD2
SMRiA1RPD2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni75 – 76Substrate bindingUniRule annotation2
Regioni209 – 210Substrate bindingUniRule annotation2
Regioni219 – 220Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000220466
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.

A1RPD2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIQFTKMHGL GNDFMVVDGV TQNVFFSPEQ IRRLADRNFG IGFDQLLLVE
60 70 80 90 100
PPYDPDLDFH YRIFNADGSE VEQCGNGARC FARFVRNKGL TNKNKIRVST
110 120 130 140 150
SSGKMTLRLE RDGTVTVNMG VPILEPSLIP FKAKKPEKTY LLQTAQQTFL
160 170 180 190 200
CGAASMGNPH CVLDVEDVAS AAVAEIGALL TKHERFPRGV NVGFMQVINS
210 220 230 240 250
GHIKLRVYER GAAETLACGT GACAAVVVGQ IQGKLDQQVR VDLPGGTLTI
260 270
NWEGEGKPLW MTGPAQHVYD GQIQL
Length:275
Mass (Da):30,125
Last modified:February 6, 2007 - v1
Checksum:i1869A8C88D51CCE0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000503 Genomic DNA Translation: ABM26527.1
RefSeqiWP_011790958.1, NC_008750.1

Genome annotation databases

EnsemblBacteriaiABM26527; ABM26527; Sputw3181_3721
KEGGishw:Sputw3181_3721

Similar proteinsi

Entry informationi

Entry nameiDAPF_SHESW
AccessioniPrimary (citable) accession number: A1RPD2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: February 6, 2007
Last modified: March 28, 2018
This is version 67 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

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

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