Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Gemmatimonas aurantiaca (strain T-27 / DSM 14586 / JCM 11422 / NBRC 100505)
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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111SubstrateUniRule annotation
Binding sitei46 – 461SubstrateUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Active sitei74 – 741Proton donor/acceptorUniRule annotation
Sitei148 – 1481Important for catalytic activityUniRule annotation
Binding sitei180 – 1801SubstrateUniRule annotation
Sitei198 – 1981Important for catalytic activityUniRule annotation
Active sitei208 – 2081Proton donor/acceptorUniRule annotation

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciGAUR379066:GI3W-1640-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:GAU_1611
OrganismiGemmatimonas aurantiaca (strain T-27 / DSM 14586 / JCM 11422 / NBRC 100505)
Taxonomic identifieri379066 [NCBI]
Taxonomic lineageiBacteriaGemmatimonadetesGemmatimonadalesGemmatimonadaceaeGemmatimonas
ProteomesiUP000002209 Componenti: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 277277Diaminopimelate epimerasePRO_1000204061Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi74 ↔ 208

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi379066.GAU_1611.

Structurei

3D structure databases

ProteinModelPortaliC1A8U3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni74 – 763Substrate bindingUniRule annotation
Regioni198 – 1992Substrate 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.
InterProiIPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.

Sequencei

Sequence statusi: Complete.

C1A8U3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFVKMTGSG NDFVFFDGRT TPIDLVTQPE AIKAICNRYN GIGADGLVVL
60 70 80 90 100
EPLQEEADVR VHYYNSDGTA ADLCGNATLC STAISAQWGI TSASGMRLAT
110 120 130 140 150
GAGLINSRID GLPAIALQPI TDIRPDMPIA PATAQGRRVG FAVAGIPHLV
160 170 180 190 200
ILCEDADAVD VAGAGPALRR HEATGPAGAN VNWVSPRPDG SWRYRTFERG
210 220 230 240 250
VEGETLACGT GAVATAVLLR SWGLSDGATT TIRTSSGRDV EVDLEPLTAP
260 270
DGRSLEGFRP TLRGEGRVVF RGEIAGL
Length:277
Mass (Da):28,993
Last modified:May 26, 2009 - v1
Checksum:i729354861C6A19DF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009153 Genomic DNA. Translation: BAH38653.1.
RefSeqiYP_002761123.1. NC_012489.1.

Genome annotation databases

EnsemblBacteriaiBAH38653; BAH38653; GAU_1611.
KEGGigau:GAU_1611.
PATRICi21956116. VBIGemAur55831_1657.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009153 Genomic DNA. Translation: BAH38653.1.
RefSeqiYP_002761123.1. NC_012489.1.

3D structure databases

ProteinModelPortaliC1A8U3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi379066.GAU_1611.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAH38653; BAH38653; GAU_1611.
KEGGigau:GAU_1611.
PATRICi21956116. VBIGemAur55831_1657.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiHEGFGAD.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciGAUR379066:GI3W-1640-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Complete genome sequence of Gemmatimonas aurantiaca T-27 that represents a novel phylum Gemmatimonadetes."
    Takasaki K., Ichikawa N., Miura H., Matsushita S., Watanabe Y., Oguchi A., Ankai A., Yashiro I., Takahashi M., Terui Y., Fukui S., Yokoyama H., Tanikawa S., Hanada S., Kamagata Y., Fujita N.
    Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: T-27 / DSM 14586 / JCM 11422 / NBRC 100505.

Entry informationi

Entry nameiDAPF_GEMAT
AccessioniPrimary (citable) accession number: C1A8U3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: May 26, 2009
Last modified: April 1, 2015
This is version 36 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.