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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
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.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 sitei15SubstrateUniRule annotation1
Binding sitei47SubstrateUniRule annotation1
Binding sitei67SubstrateUniRule annotation1
Active sitei76Proton donorUniRule annotation1
Binding sitei163SubstrateUniRule annotation1
Sitei165Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei197SubstrateUniRule annotation1
Sitei215Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei224Proton acceptorUniRule annotation1

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 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:R03239
ORF Names:SMc03856
OrganismiRhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Taxonomic identifieri266834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
Proteomesi
  • UP000001976 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498651 – 301Diaminopimelate epimeraseAdd BLAST301

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi266834.SMc03856.

Structurei

3D structure databases

ProteinModelPortaliQ92L46.
SMRiQ92L46.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni77 – 78Substrate bindingUniRule annotation2
Regioni215 – 216Substrate bindingUniRule annotation2
Regioni225 – 226Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.

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.

Q92L46-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGDQVQFARM NGLGNKILVV DMRGRKDRVT PQAAIALNAD PATEFDQIMA
60 70 80 90 100
IHDPKSAGTD AWIDIVNSDG SMAQACGNGT RCVVQALAAE TGRKAFLFHT
110 120 130 140 150
VAGLLEAKEH DNGTISVDMG KPRFGWDQIP LAEEFHDTRR IELQIGPIDA
160 170 180 190 200
PVLHSPSVAS MGNPHAIFWV ENDVWSYELD RFGPLLENHP IFPERANISI
210 220 230 240 250
ARIRSRQEMD LRTWERGAGL TLACGSAACA AAVNGARTGR TERMVTVNVP
260 270 280 290 300
GGPLKIEWRE RDDHVIMTGP AEWEWSGTVD PVTGIFARNE PESGDNGARA

L
Length:301
Mass (Da):32,859
Last modified:June 6, 2002 - v2
Checksum:i10FA2308A713FFD8
GO

Sequence cautioni

The sequence CAC47818 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL591688 Genomic DNA. Translation: CAC47818.1. Different initiation.
RefSeqiNP_387345.1. NC_003047.1.
WP_010970515.1. NC_003047.1.

Genome annotation databases

EnsemblBacteriaiCAC47818; CAC47818; SMc03856.
GeneIDi1234933.
KEGGisme:SMc03856.
PATRICi23636140. VBISinMel96828_4792.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL591688 Genomic DNA. Translation: CAC47818.1. Different initiation.
RefSeqiNP_387345.1. NC_003047.1.
WP_010970515.1. NC_003047.1.

3D structure databases

ProteinModelPortaliQ92L46.
SMRiQ92L46.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi266834.SMc03856.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAC47818; CAC47818; SMc03856.
GeneIDi1234933.
KEGGisme:SMc03856.
PATRICi23636140. VBISinMel96828_4792.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

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.
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_RHIME
AccessioniPrimary (citable) accession number: Q92L46
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 6, 2002
Last sequence update: June 6, 2002
Last modified: March 15, 2017
This is version 79 of the entry and version 2 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.