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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Caulobacter sp. (strain K31)
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:iL-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 sitei13 – 131SubstrateUniRule annotation
Binding sitei52 – 521SubstrateUniRule annotation
Binding sitei72 – 721SubstrateUniRule annotation
Active sitei81 – 811Proton donor/acceptorUniRule annotation
Binding sitei167 – 1671SubstrateUniRule annotation
Sitei169 – 1691Important for catalytic activityUniRule annotation
Binding sitei201 – 2011SubstrateUniRule annotation
Sitei219 – 2191Important for catalytic activityUniRule annotation
Active sitei228 – 2281Proton 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

BioCyciCSP366602:GH0Y-4921-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:Caul_4868
OrganismiCaulobacter sp. (strain K31)
Taxonomic identifieri366602 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaeCaulobacter
ProteomesiUP000001316 Componenti: Chromosome

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 – 289289Diaminopimelate epimerasePRO_1000077693Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi81 ↔ 228

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi366602.Caul_4868.

Structurei

3D structure databases

ProteinModelPortaliB0T542.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni81 – 833Substrate bindingUniRule annotation
Regioni219 – 2202Substrate bindingUniRule annotation
Regioni229 – 2302Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiGMGNPHC.
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.

B0T542-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRTFLKMNG LGNDFVVIET LTQPFHPTAE EIRAIAKRPN AKEGEGGIGC
60 70 80 90 100
DQVIAIDPPR AEGASAYVRF WNSDGEETGA CGNGTRCVAW LLMQSGQKDS
110 120 130 140 150
VAFDTVAGRL SGKMAGDKLV TVDMGQPGLA WNQIPLAEEM DTVGIELQVG
160 170 180 190 200
PIDAPLVHTP GCVSMGNPHV VFFVDAPVSD AFARGTGSLV EHHPLFPEGV
210 220 230 240 250
NVGFAHIAAR DHIKLKVWER GAGLTAACGT GACAAQVAAV RRGLTDRVAK
260 270 280
VEFESGALTI EWREADGHVI MTGPVTMEFV GKLPEKVAA
Length:289
Mass (Da):30,572
Last modified:April 8, 2008 - v1
Checksum:i519E9067971B0C62
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000927 Genomic DNA. Translation: ABZ73988.1.
RefSeqiWP_012288859.1. NC_010338.1.

Genome annotation databases

EnsemblBacteriaiABZ73988; ABZ73988; Caul_4868.
KEGGicak:Caul_4868.
PATRICi21322920. VBICauSp18104_5282.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000927 Genomic DNA. Translation: ABZ73988.1.
RefSeqiWP_012288859.1. NC_010338.1.

3D structure databases

ProteinModelPortaliB0T542.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi366602.Caul_4868.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABZ73988; ABZ73988; Caul_4868.
KEGGicak:Caul_4868.
PATRICi21322920. VBICauSp18104_5282.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiGMGNPHC.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciCSP366602:GH0Y-4921-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K31.

Entry informationi

Entry nameiDAPF_CAUSK
AccessioniPrimary (citable) accession number: B0T542
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: April 8, 2008
Last modified: July 22, 2015
This is version 49 of the entry and version 1 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.