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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Pelagibacter ubique (strain HTCC1062)
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 sitei13 – 131SubstrateUniRule annotation
Binding sitei45 – 451SubstrateUniRule annotation
Binding sitei63 – 631SubstrateUniRule annotation
Active sitei72 – 721Proton 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

BioCyciCPEL335992:GH3Z-257-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:SAR11_0257
OrganismiPelagibacter ubique (strain HTCC1062)
Taxonomic identifieri335992 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSAR11 clusterCandidatus Pelagibacter
ProteomesiUP000002528 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 – 274274Diaminopimelate epimerasePRO_1000011923Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi72 ↔ 218

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi335992.SAR11_0257.

Structurei

3D structure databases

ProteinModelPortaliQ4FP10.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni72 – 743Substrate bindingUniRule annotation
Regioni209 – 2102Substrate bindingUniRule annotation
Regioni219 – 2202Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiWMELIGN.
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.

Q4FP10-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDIKAFKMDG LGNDFVIIDQ RSQDFNLDKD QIIKICDRSF IGCDQLILIK
60 70 80 90 100
KNKEIDANVE FFNSDGSISG ACGNGTRCVA DLLSKESGKK EITLLTTSGS
110 120 130 140 150
LKSKILGNNL VETEIGIPKV NWQEIPLSKQ LDTQDLKIEI IDRNNTKHIG
160 170 180 190 200
GIAINVGNPH IIFFVDDIEA FDLKNIGPKI ENHPLFPEKC NVTLAKVINR
210 220 230 240 250
NLIKVKVWER GAGLTKACGT AACATAVAAN INNLVEKTTD IEFVLGSLTI
260 270
SIDERNSIHM KGPVSDIKNI NIKL
Length:274
Mass (Da):30,102
Last modified:August 30, 2005 - v1
Checksum:i4DDA04FC3A543FB6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000084 Genomic DNA. Translation: AAZ21079.1.
RefSeqiWP_011281577.1. NC_007205.1.
YP_265682.1. NC_007205.1.

Genome annotation databases

EnsemblBacteriaiAAZ21079; AAZ21079; SAR11_0257.
KEGGipub:SAR11_0257.
PATRICi31989971. VBICanPel5618_0256.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000084 Genomic DNA. Translation: AAZ21079.1.
RefSeqiWP_011281577.1. NC_007205.1.
YP_265682.1. NC_007205.1.

3D structure databases

ProteinModelPortaliQ4FP10.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi335992.SAR11_0257.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAZ21079; AAZ21079; SAR11_0257.
KEGGipub:SAR11_0257.
PATRICi31989971. VBICanPel5618_0256.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiWMELIGN.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciCPEL335992:GH3Z-257-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: HTCC1062.

Entry informationi

Entry nameiDAPF_PELUB
AccessioniPrimary (citable) accession number: Q4FP10
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: August 30, 2005
Last modified: April 1, 2015
This is version 64 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.