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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Prochlorococcus marinus (strain NATL1A)
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 sitei70SubstrateUniRule annotation1
Active sitei79Proton donorUniRule annotation1
Binding sitei167SubstrateUniRule annotation1
Sitei169Could 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

BioCyciPMAR167555:G1G7Z-956-MONOMER
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:NATL1_09951
OrganismiProchlorococcus marinus (strain NATL1A)
Taxonomic identifieri167555 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaSynechococcalesProchloraceaeProchlorococcus
Proteomesi
  • UP000002592 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119261 – 284Diaminopimelate epimeraseAdd BLAST284

Proteomic databases

PRIDEiA2C243

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi167555.NATL1_09951

Structurei

3D structure databases

ProteinModelPortaliA2C243
SMRiA2C243
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni80 – 81Substrate 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
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.

A2C243-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKNNFSKYQG LGNDFIIFDA RSNNLDHLFS KNKDNFIEHL CNRNFGIGAD
60 70 80 90 100
GIILILESNN KCFVRMKIYN SDGSEPEMCG NGIRCLIAFL NDNNEINELS
110 120 130 140 150
EIPIETKAGL ILTSIDCNEN IKVNMGEPIL SPLDIPTKLL MNSLKVPNGV
160 170 180 190 200
ITLKDQILNV YAASMGNPHM IVFVNDIEGI PFQEWGSFLE KHNTFPNDTN
210 220 230 240 250
VHFVEIIDKS NIKVKVWERG CGPTLACGTG ACACLVVTSK LGKTLNNANV
260 270 280
YLPGGKLEVE WPNQSGPVFM QGPALKVFSG EIDI
Length:284
Mass (Da):31,369
Last modified:February 20, 2007 - v1
Checksum:iA6E8CA18106B52FD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000553 Genomic DNA Translation: ABM75553.1
RefSeqiWP_011823679.1, NC_008819.1

Genome annotation databases

EnsemblBacteriaiABM75553; ABM75553; NATL1_09951
KEGGipme:NATL1_09951

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000553 Genomic DNA Translation: ABM75553.1
RefSeqiWP_011823679.1, NC_008819.1

3D structure databases

ProteinModelPortaliA2C243
SMRiA2C243
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi167555.NATL1_09951

Proteomic databases

PRIDEiA2C243

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABM75553; ABM75553; NATL1_09951
KEGGipme:NATL1_09951

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
HOGENOMiHOG000220466
KOiK01778
OMAiSMCGNGG
OrthoDBiPOG091H01QC

Enzyme and pathway databases

UniPathwayi
UPA00034;UER00025

BioCyciPMAR167555:G1G7Z-956-MONOMER

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_PROM1
AccessioniPrimary (citable) accession number: A2C243
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: February 20, 2007
Last modified: October 10, 2018
This is version 70 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

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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