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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methanothrix thermoacetophila (strain DSM 6194 / JCM 14653 / NBRC 101360 / PT) (Methanosaeta thermophila)
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.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 sitei14SubstrateUniRule annotation1
Binding sitei68SubstrateUniRule annotation1
Active sitei77Proton donorUniRule annotation1
Sitei161Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei191SubstrateUniRule 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

UniPathwayi
UPA00034;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:Mthe_0454
OrganismiMethanothrix thermoacetophila (strain DSM 6194 / JCM 14653 / NBRC 101360 / PT) (Methanosaeta thermophila)
Taxonomic identifieri349307 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaStenosarchaea groupMethanomicrobiaMethanosarcinalesMethanosaetaceaeMethanothrix
Proteomesi
  • UP000000674 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119051 – 279Diaminopimelate epimeraseAdd BLAST279

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi349307.Mthe_0454

Structurei

3D structure databases

ProteinModelPortaliA0B6C1
SMRiA0B6C1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni78 – 79Substrate bindingUniRule annotation2
Regioni207 – 208Substrate bindingUniRule annotation2
Regioni218 – 219Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiarCOG02255 Archaea
COG0253 LUCA
HOGENOMiHOG000220466
KOiK01778
OMAiSMCGNGG
OrthoDBiPOG093Z085A

Family and domain databases

HAMAPiMF_00197 DAP_epimerase, 1 hit
InterProiView protein in InterPro
IPR001653 DAP_epimerase_DapF
PANTHERiPTHR31689 PTHR31689, 1 hit
PfamiView protein in Pfam
PF01678 DAP_epimerase, 2 hits
TIGRFAMsiTIGR00652 DapF, 1 hit

Sequencei

Sequence statusi: Complete.

A0B6C1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNQLEFVKLH GNGNDFILID ELNGERIPED EKSEASRILC HRNFGIGGDG
60 70 80 90 100
VLFLVPSERA DIGMRLFQPD GSEAEMCGNG IRCLAKHAWE SGYVGERFSV
110 120 130 140 150
ETLAGVIPIQ VRRDRKGFWA RVEMGIPRFE RSEIPADGEG TFLKVPLHGF
160 170 180 190 200
EVSAVNTGVP HAVIFVENLD IPVEQIAPKI RHSSCFPEGA NVNFVRLGNH
210 220 230 240 250
LEVRTFERGV EAETLSCGTG SVAAAAVARR LGLVGETVEV MTKGGPLRIS
260 270
FAGEKAFMEG PAVTVCRGVV SDEILQTLQ
Length:279
Mass (Da):30,386
Last modified:November 28, 2006 - v1
Checksum:iF1CF018283554695
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000477 Genomic DNA Translation: ABK14245.1

Genome annotation databases

EnsemblBacteriaiABK14245; ABK14245; Mthe_0454
KEGGimtp:Mthe_0454

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000477 Genomic DNA Translation: ABK14245.1

3D structure databases

ProteinModelPortaliA0B6C1
SMRiA0B6C1
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi349307.Mthe_0454

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK14245; ABK14245; Mthe_0454
KEGGimtp:Mthe_0454

Phylogenomic databases

eggNOGiarCOG02255 Archaea
COG0253 LUCA
HOGENOMiHOG000220466
KOiK01778
OMAiSMCGNGG
OrthoDBiPOG093Z085A

Enzyme and pathway databases

UniPathwayi
UPA00034;UER00025

Family and domain databases

HAMAPiMF_00197 DAP_epimerase, 1 hit
InterProiView protein in InterPro
IPR001653 DAP_epimerase_DapF
PANTHERiPTHR31689 PTHR31689, 1 hit
PfamiView protein in Pfam
PF01678 DAP_epimerase, 2 hits
TIGRFAMsiTIGR00652 DapF, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_METTP
AccessioniPrimary (citable) accession number: A0B6C1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 28, 2006
Last modified: October 10, 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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Main funding by: National Institutes of Health

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