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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
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 sitei11SubstrateUniRule annotation1
Binding sitei78SubstrateUniRule annotation1
Active sitei87Proton donorUniRule annotation1
Binding sitei166SubstrateUniRule annotation1
Sitei168Could 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

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciMSME246196:G1H7P-2734-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:MSMEG_2735, MSMEI_2668
OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Taxonomic identifieri246196 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium fortuitum complex
Proteomesi
  • UP000006158 Componenti: Chromosome
  • UP000000757 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119091 – 291Diaminopimelate epimeraseAdd BLAST291

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi246196.MSMEG_2735

Structurei

3D structure databases

ProteinModelPortaliA0QVY0
SMRiA0QVY0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni88 – 89Substrate bindingUniRule annotation2
Regioni218 – 219Substrate bindingUniRule annotation2
Regioni228 – 229Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
HOGENOMiHOG000220467
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.

A0QVY0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIFAKGHGTE NDFVVLPDLD AALSLTPSAV AALCDRRRGL GADGVLRVTR
60 70 80 90 100
AGAARAAGVF DRLPDGVSAG DWYMDYRNAD GSIAQMCGNG VRVFAHYLRA
110 120 130 140 150
SGLESADEFV VGSLAGPRPV VLHGFDPARA TTAEVTVEMG KANQFGAGSA
160 170 180 190 200
VVGGRSFDGL AVDVGNPHLA CVGITADDLA ALDVAAPVSF DPALFPDGVN
210 220 230 240 250
VEVLTASVDG AVSMRVHERG VGETRSCGTG TVAATVAALA HDGADTGTLR
260 270 280 290
VRIPGGEVTV TVTESTSYLR GPSVLVARGE LDPHWWHAVA G
Length:291
Mass (Da):29,791
Last modified:January 9, 2007 - v1
Checksum:iBB63840A5B690C9D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA Translation: ABK73529.1
CP001663 Genomic DNA Translation: AFP39136.1
RefSeqiWP_011728551.1, NZ_CP009494.1
YP_887068.1, NC_008596.1

Genome annotation databases

EnsemblBacteriaiABK73529; ABK73529; MSMEG_2735
AFP39136; AFP39136; MSMEI_2668
GeneIDi4533230
KEGGimsb:LJ00_13600
msg:MSMEI_2668
msm:MSMEG_2735
PATRICifig|246196.19.peg.2703

Similar proteinsi

Entry informationi

Entry nameiDAPF_MYCS2
AccessioniPrimary (citable) accession number: A0QVY0
Secondary accession number(s): I7G799
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: January 9, 2007
Last modified: May 23, 2018
This is version 75 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

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