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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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 sitei11Substrate1
Binding sitei44Substrate1
Binding sitei64Substrate1
Active sitei73Proton donor1
Binding sitei157Substrate1
Sitei159Could be important to modulate the pK values of the two catalytic cysteine residues1
Binding sitei190Substrate1
Sitei208Could be important to modulate the pK values of the two catalytic cysteine residues1
Active sitei217Proton acceptor1
Sitei268Important 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:STM3947
ORF Names:STMD1.43
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498691 – 274Diaminopimelate epimeraseAdd BLAST274

Proteomic databases

PaxDbiP0A1F2.
PRIDEiP0A1F2.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi99287.STM3947.

Structurei

3D structure databases

ProteinModelPortaliP0A1F2.
SMRiP0A1F2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni74 – 75Substrate binding2
Regioni208 – 209Substrate binding2
Regioni218 – 219Substrate binding2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMCGNGGR.
PhylomeDBiP0A1F2.

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.

P0A1F2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQFSKMHGLG NDFMVVDAVT QNVFFSPELI RRLSDRHLGV GFDQLLVVEP
60 70 80 90 100
PYDPELDFHY RIFNADGSEV SQCGNGARCF ARFVRLKGLT NKRDIRVSTA
110 120 130 140 150
NGRMVLSVTE DELVRVNMGE PNFEPAQVPF RANKAEKTYI MRAAEQTILC
160 170 180 190 200
GVVSMGNPHC VIQVDNVDTA AVETLGPVLE SHERFPERAN IGFMQVVRRE
210 220 230 240 250
HIRLRVYERG AGETRACGSG ACAAVAVGIQ QGLLAEEVRV ELPGGRLDIA
260 270
WKGPGHPLYM TGPAAHIYDG FIHL
Length:274
Mass (Da):30,337
Last modified:March 1, 2005 - v1
Checksum:i2FBB315B7DA12AE9
GO

Sequence cautioni

The sequence AAF33445 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence AAL22791 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF233324 Genomic DNA. Translation: AAF33445.1. Different initiation.
AE006468 Genomic DNA. Translation: AAL22791.1. Different initiation.
RefSeqiNP_462832.3. NC_003197.2.

Genome annotation databases

EnsemblBacteriaiAAL22791; AAL22791; STM3947.
GeneIDi1255473.
KEGGistm:STM3947.
PATRICifig|99287.12.peg.4165.

Similar proteinsi

Entry informationi

Entry nameiDAPF_SALTY
AccessioniPrimary (citable) accession number: P0A1F2
Secondary accession number(s): Q9L6P6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2005
Last modified: November 22, 2017
This is version 84 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