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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Hydrogenobaculum sp. (strain Y04AAS1)
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 sitei72SubstrateUniRule annotation1
Active sitei81Proton donorUniRule annotation1
Sitei155Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei189SubstrateUniRule annotation1
Sitei207Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei217Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciHSP380749:G1GCJ-1187-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:HY04AAS1_1165
OrganismiHydrogenobaculum sp. (strain Y04AAS1)
Taxonomic identifieri380749 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeHydrogenobaculum
Proteomesi
  • UP000001872 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992431 – 277Diaminopimelate epimeraseAdd BLAST277

Proteomic databases

PRIDEiB4U9P0

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi380749.HY04AAS1_1165

Structurei

3D structure databases

ProteinModelPortaliB4U9P0
SMRiB4U9P0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni82 – 83Substrate bindingUniRule annotation2
Regioni207 – 208Substrate bindingUniRule annotation2
Regioni218 – 219Substrate 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.

B4U9P0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLITKYQGSG NDFIIIDNRD NFVYKEIEKL GLSINEFVRK LCEQHTSVGA
60 70 80 90 100
DGVILIEKAR NTKNHFSWAF FNADGSAAEM CGNGSRCAAR FAYEKDIAPK
110 120 130 140 150
DIVFETIAGE IEAHIMDSKR VKVQLTPYHS HQKNIEIKTE YGTFKGHFVN
160 170 180 190 200
TGVPHFVIFV DEDELDNLDV EKVGRAIRYH EYFAPKGTNV NFVAKTKNGS
210 220 230 240 250
FRIRTYERGV EGETLACGTG SAACGINAYL LGLSASNIVD IITKSGELLK
260 270
ITIENDKVFL EGPTTKVFEG MLSYEIF
Length:277
Mass (Da):30,932
Last modified:September 23, 2008 - v1
Checksum:i2A43015B831A96A9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001130 Genomic DNA Translation: ACG57851.1
RefSeqiWP_012514207.1, NC_011126.1

Genome annotation databases

EnsemblBacteriaiACG57851; ACG57851; HY04AAS1_1165
KEGGihya:HY04AAS1_1165

Similar proteinsi

Entry informationi

Entry nameiDAPF_HYDS0
AccessioniPrimary (citable) accession number: B4U9P0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 23, 2008
Last modified: May 23, 2018
This is version 56 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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