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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Psychrobacter arcticus (strain DSM 17307 / 273-4)
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 sitei13SubstrateUniRule annotation1
Binding sitei46SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donorUniRule annotation1
Binding sitei162SubstrateUniRule annotation1
Sitei164Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei195SubstrateUniRule annotation1
Sitei213Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei222Proton acceptorUniRule annotation1
Sitei274Important for dimerizationUniRule 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:Psyc_0200
OrganismiPsychrobacter arcticus (strain DSM 17307 / 273-4)
Taxonomic identifieri259536 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesMoraxellaceaePsychrobacter
Proteomesi
  • UP000000546 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119381 – 295Diaminopimelate epimeraseAdd BLAST295

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi259536.Psyc_0200.

Structurei

3D structure databases

ProteinModelPortaliQ4FV85.
SMRiQ4FV85.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate bindingUniRule annotation2
Regioni213 – 214Substrate bindingUniRule annotation2
Regioni223 – 224Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

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

Q4FV85-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLIEFTKMHG LGNDFMVIDL VTQRLDLTKD LVQLLGDRHL GIGFDQLLVV
60 70 80 90 100
EPPMRPDVDF SYRIFNTDGT EVEQCGNGAR CFARFVQARK LSFKQRLRVE
110 120 130 140 150
TASGIISLTT DHYGWVEVDM GKPKFEPSEI PFTPRATTKI QNAYHLDVNG
160 170 180 190 200
TPVQLYVANM GNPHAVIKVD DVLDADVESL GRAIESHPAF PERVNVGFMQ
210 220 230 240 250
VMNQRHIRLR VYERGVGETQ ACGTGACAAV AIGIREGWLD EGEDVRAQLY
260 270 280 290
GGSMVIKWQP GYSVMMTGPT AFVYEGVFSP DGLMAQAGIK PNPEI
Length:295
Mass (Da):32,721
Last modified:August 30, 2005 - v1
Checksum:iA7321B5C1403C906
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000082 Genomic DNA. Translation: AAZ18073.1.
RefSeqiWP_011279512.1. NC_007204.1.

Genome annotation databases

EnsemblBacteriaiAAZ18073; AAZ18073; Psyc_0200.
KEGGipar:Psyc_0200.

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.

Entry informationi

Entry nameiDAPF_PSYA2
AccessioniPrimary (citable) accession number: Q4FV85
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: August 30, 2005
Last modified: June 7, 2017
This is version 75 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