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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Flavobacterium psychrophilum (strain JIP02/86 / ATCC 49511)
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 sitei11SubstrateUniRule annotation1
Binding sitei63SubstrateUniRule annotation1
Active sitei72Proton donorUniRule annotation1
Sitei137Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei169SubstrateUniRule annotation1
Sitei187Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei197Proton 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:FP1215
OrganismiFlavobacterium psychrophilum (strain JIP02/86 / ATCC 49511)
Taxonomic identifieri402612 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesFlavobacteriiaFlavobacterialesFlavobacteriaceaeFlavobacterium
Proteomesi
  • UP000006394 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992371 – 256Diaminopimelate epimeraseAdd BLAST256

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi402612.FP1215.

Structurei

3D structure databases

ProteinModelPortaliA6GYX5.
SMRiA6GYX5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni73 – 74Substrate bindingUniRule annotation2
Regioni187 – 188Substrate bindingUniRule annotation2
Regioni198 – 199Substrate 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.

A6GYX5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLYKYQGTG NDFIMIDNRL QIFPKQNTAL IQKLCDRRFG IGADGLILLE
60 70 80 90 100
NDQSTDFKMV YYNSDGNQST MCGNGGRCLV AFAKKLNIIK NKTTFIAIDG
110 120 130 140 150
LHHATINEND IISLQMKNVE EVNIHDNYVF LNTGSPHHVQ FADNLSNFDV
160 170 180 190 200
KNEGAKIRYS DLYGQAGSNI NFVHQTSPTQ FSIRTYERGV EDETLSCGTG
210 220 230 240 250
ATATAIAMKA TGKTNSNNIT INVQGGKLEV SFNQENSIFT NIFLKGPAEF

VFETTI
Length:256
Mass (Da):28,463
Last modified:July 24, 2007 - v1
Checksum:i42633776D96E3A8B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM398681 Genomic DNA. Translation: CAL43298.1.
RefSeqiWP_011963347.1. NC_009613.3.
YP_001296109.1. NC_009613.3.

Genome annotation databases

EnsemblBacteriaiCAL43298; CAL43298; FP1215.
GeneIDi5298992.
KEGGifps:FP1215.
PATRICifig|402612.5.peg.1229.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM398681 Genomic DNA. Translation: CAL43298.1.
RefSeqiWP_011963347.1. NC_009613.3.
YP_001296109.1. NC_009613.3.

3D structure databases

ProteinModelPortaliA6GYX5.
SMRiA6GYX5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi402612.FP1215.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL43298; CAL43298; FP1215.
GeneIDi5298992.
KEGGifps:FP1215.
PATRICifig|402612.5.peg.1229.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMCGNGGR.
OrthoDBiPOG091H01QC.

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_FLAPJ
AccessioniPrimary (citable) accession number: A6GYX5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 24, 2007
Last modified: June 7, 2017
This is version 62 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

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.