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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
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 sitei160SubstrateUniRule annotation1
Sitei162Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei193SubstrateUniRule annotation1
Sitei211Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei220Proton acceptorUniRule annotation1
Sitei271Important 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:lpg0366
OrganismiLegionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
Taxonomic identifieri272624 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaLegionellalesLegionellaceaeLegionella
Proteomesi
  • UP000000609 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000118951 – 277Diaminopimelate epimeraseAdd BLAST277

Proteomic databases

PaxDbiQ5ZYK6.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi272624.lpg0366.

Structurei

3D structure databases

ProteinModelPortaliQ5ZYK6.
SMRiQ5ZYK6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate bindingUniRule annotation2
Regioni211 – 212Substrate bindingUniRule annotation2
Regioni221 – 222Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

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

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiView protein in InterPro
IPR001653. DAP_epimerase_DapF.
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiView protein in Pfam
PF01678. DAP_epimerase. 2 hits.
TIGRFAMsiTIGR00652. DapF. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5ZYK6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGIKFTKMHG LGNDFIVLDG VNQSIQLTVE QIQKLANRHT GIGFDQCLLI
60 70 80 90 100
ESSQTEGIDF NYRIFNADGQ EVGQCGNGAR CIALFARYYG LTAKNKLTVA
110 120 130 140 150
TKTTLMDLII NEDNSVSVNM GVPRLAPGEI PLLADRQSPE YSLELNNGNT
160 170 180 190 200
VNLHAISVGN PHAVLLVENI DTAPVNSLGQ QISFHPQFPE QVNVGFMQII
210 220 230 240 250
NHEKINLRVY ERGCGETIAC GSGAVAAAAI ARLFYNLSDK ITVHLPGGDL
260 270
CIQWPCPTAP IILTGPAAFV YEGTLLS
Length:277
Mass (Da):29,953
Last modified:November 23, 2004 - v1
Checksum:iDE73BE862397C9A7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017354 Genomic DNA. Translation: AAU26463.1.
RefSeqiWP_010946115.1. NC_002942.5.
YP_094410.1. NC_002942.5.

Genome annotation databases

EnsemblBacteriaiAAU26463; AAU26463; lpg0366.
GeneIDi19831932.
KEGGilpn:lpg0366.
PATRICifig|272624.6.peg.373.

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_LEGPH
AccessioniPrimary (citable) accession number: Q5ZYK6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 23, 2004
Last modified: June 7, 2017
This is version 80 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