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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Alkaliphilus oremlandii (strain OhILAs) (Clostridium oremlandii (strain OhILAs))
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 sitei13SubstrateUniRule annotation1
Binding sitei65SubstrateUniRule annotation1
Active sitei74Proton donorUniRule annotation1
Sitei165Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei196SubstrateUniRule annotation1
Sitei214Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei223Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciAORE350688:G1GAA-1476-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:Clos_1420
OrganismiAlkaliphilus oremlandii (strain OhILAs) (Clostridium oremlandii (strain OhILAs))
Taxonomic identifieri350688 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesClostridiaceaeAlkaliphilus
Proteomesi

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000585361 – 280Diaminopimelate epimeraseAdd BLAST280

Proteomic databases

PRIDEiA8MH77

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi350688.Clos_1420

Structurei

3D structure databases

ProteinModelPortaliA8MH77
SMRiA8MH77
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni75 – 76Substrate bindingUniRule annotation2
Regioni214 – 215Substrate bindingUniRule annotation2
Regioni224 – 225Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
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.

A8MH77-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDVQFKKMQG TGNDFIVVKY DDFPFEEKLS QLAEKICDRH FGIGADGLLI
60 70 80 90 100
VNPSSIADIR MDYYNSDGSI AAMCGNGIRC FSKFVFDEGF LRTKQFSVET
110 120 130 140 150
LDGIKEIAII EEKGTVKSVE VNMGQVTYDT EKIPVVSEDG YFINKKITVG
160 170 180 190 200
GQDFIITAVS MGVPHVIIFT EKLDLEQIKF FGPLIEKHAI FPKKTNVNFV
210 220 230 240 250
HRIDKDNIAV RTWERGAGYT LACGTGSTSA VAVANKLGLV NNNVNVEVEG
260 270 280
GNIKIKIKES GNLFMEGPAE NICSGRFFFN
Length:280
Mass (Da):30,983
Last modified:December 4, 2007 - v1
Checksum:iA250AE65EC4C2419
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000853 Genomic DNA Translation: ABW18964.1
RefSeqiWP_012159276.1, NC_009922.1

Genome annotation databases

EnsemblBacteriaiABW18964; ABW18964; Clos_1420
KEGGiaoe:Clos_1420

Similar proteinsi

Entry informationi

Entry nameiDAPF_ALKOO
AccessioniPrimary (citable) accession number: A8MH77
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: December 4, 2007
Last modified: May 23, 2018
This is version 58 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

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