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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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

Pathway: 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei20 – 201SubstrateUniRule annotation
Binding sitei54 – 541SubstrateUniRule annotation
Binding sitei72 – 721SubstrateUniRule annotation
Active sitei81 – 811Proton donor/acceptorUniRule annotation
Binding sitei158 – 1581SubstrateUniRule annotation
Sitei160 – 1601Important for catalytic activityUniRule annotation
Binding sitei191 – 1911SubstrateUniRule annotation
Sitei209 – 2091Important for catalytic activityUniRule annotation
Active sitei218 – 2181Proton donor/acceptorUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciRSPH272943:GJAS-2611-MONOMER.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:RHOS4_25500
ORF Names:RSP_0936
OrganismiRhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
Taxonomic identifieri272943 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter
ProteomesiUP000002703 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 279279Diaminopimelate epimerasePRO_1000071716Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi81 ↔ 218

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi272943.RSP_0936.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni81 – 833Substrate bindingUniRule annotation
Regioni209 – 2102Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiHEGFGAD.
OrthoDBiEOG6ND0M5.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q3IZB6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMDMGASSGL GFMKMHGAGN DFVVIDSRGR GGALVTAGLA RALGDRHRGV
60 70 80 90 100
GFDQLAEIRD QEGADCALDF WNSDGSRSGT CGNATRCVSD YLMRDLGRDE
110 120 130 140 150
VNLVTARGRL HARRREDGLV AVNMGAPQLL WSEIPLARAM ETDSLPLEGT
160 170 180 190 200
PSAVGMGNPH CIYFVEDAEA VDLAGRGAAV ETDPLFPERT NVEFASLIGP
210 220 230 240 250
DRLRLRVWER GAGITLACGS GACATAVAAA RRGLTGRQVR LEMDGGVLEV
260 270
DWRDEGVWLS GPVARVFEGH LSPEMMALA
Length:279
Mass (Da):29,744
Last modified:February 19, 2014 - v2
Checksum:i258D2D8B4CD915D2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000143 Genomic DNA. Translation: ABA80118.2.
RefSeqiWP_017139968.1. NZ_AKVW01000001.1.
YP_354019.2. NC_007493.2.

Genome annotation databases

EnsemblBacteriaiABA80118; ABA80118; RSP_0936.
GeneIDi3717923.
KEGGirsp:RSP_0936.
PATRICi23155071. VBIRhoSph57909_2904.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000143 Genomic DNA. Translation: ABA80118.2.
RefSeqiWP_017139968.1. NZ_AKVW01000001.1.
YP_354019.2. NC_007493.2.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272943.RSP_0936.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA80118; ABA80118; RSP_0936.
GeneIDi3717923.
KEGGirsp:RSP_0936.
PATRICi23155071. VBIRhoSph57909_2904.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiHEGFGAD.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciRSPH272943:GJAS-2611-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of chromosome 1 of Rhodobacter sphaeroides 2.4.1."
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Richardson P., Mackenzie C., Choudhary M., Larimer F., Hauser L.J., Land M., Donohue T.J., Kaplan S.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158.

Entry informationi

Entry nameiDAPF_RHOS4
AccessioniPrimary (citable) accession number: Q3IZB6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: February 19, 2014
Last modified: May 27, 2015
This is version 64 of the entry and version 2 of the sequence. [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

External Data

Dasty 3

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 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.