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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
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 sitei22SubstrateUniRule annotation1
Binding sitei56SubstrateUniRule annotation1
Binding sitei76SubstrateUniRule annotation1
Active sitei85Proton donorUniRule annotation1
Binding sitei169SubstrateUniRule annotation1
Sitei171Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei202SubstrateUniRule annotation1
Sitei220Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei229Proton acceptorUniRule annotation1
Sitei280Important for dimerizationUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciBAPH224915:G1G09-540-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:bbp_533
OrganismiBuchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
Taxonomic identifieri224915 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesErwiniaceaeBuchnera
Proteomesi

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498271 – 286Diaminopimelate epimeraseAdd BLAST286

Proteomic databases

PRIDEiP59582

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi224915.bbp533

Structurei

3D structure databases

ProteinModelPortaliP59582
SMRiP59582
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni86 – 87Substrate bindingUniRule annotation2
Regioni220 – 221Substrate bindingUniRule annotation2
Regioni230 – 231Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
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.

P59582-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHIKVVHKSV KIKFSKMHGL GNDFIIINAM MQKTFPVTSN IIQNLSNRYT
60 70 80 90 100
GIGFDQLLLV ENSKNVNIDF HYRIFNANGT EVSQCGNGAR CFALFVLLKK
110 120 130 140 150
LTKKRTLYVS TNTTTLILNV LNNGNVCVDM GVPCFKLKNI FGENIIENSL
160 170 180 190 200
HSIKFVNKII NYDLVSIGNP HCIIYVNNLK KYPVKKIGFY LSTHKIFPEG
210 220 230 240 250
INVNFVEVLS KNEIALRVYE RGVGETLACG SGACASVALG IQQGLLFNEV
260 270 280
QVNLLNGILK INWKGGSEKL YMTGPAVHVY DGYFYL
Length:286
Mass (Da):31,978
Last modified:April 11, 2003 - v1
Checksum:i9FB2231DDAD4E8A4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016826 Genomic DNA Translation: AAO27235.1
RefSeqiWP_011091636.1, NC_004545.1

Genome annotation databases

EnsemblBacteriaiAAO27235; AAO27235; bbp_533
KEGGibab:bbp_533

Similar proteinsi

Entry informationi

Entry nameiDAPF_BUCBP
AccessioniPrimary (citable) accession number: P59582
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 11, 2003
Last sequence update: April 11, 2003
Last modified: May 23, 2018
This is version 92 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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