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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
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 sitei13 – 131SubstrateUniRule annotation
Binding sitei46 – 461SubstrateUniRule annotation
Binding sitei66 – 661SubstrateUniRule annotation
Active sitei75 – 751Proton donor/acceptorUniRule annotation
Binding sitei159 – 1591SubstrateUniRule annotation
Sitei161 – 1611Important for catalytic activityUniRule annotation
Binding sitei192 – 1921SubstrateUniRule annotation
Sitei210 – 2101Important for catalytic activityUniRule annotation
Active sitei219 – 2191Proton donor/acceptorUniRule annotation

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: TIGR

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: TIGR
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-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
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:VC_0126
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000000584 Componenti: Chromosome 1

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 – 276276Diaminopimelate epimerasePRO_0000149875Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 219

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi243277.VC0126.

Structurei

3D structure databases

ProteinModelPortaliQ9KVL6.
SMRiQ9KVL6. Positions 4-275.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni75 – 773Substrate bindingUniRule annotation
Regioni210 – 2112Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
KOiK01778.
OMAiMKFTKMH.
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.

Q9KVL6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHFHFSKMHG LGNDFMVVDC ITQNVFFSPE LIRRLADRHT GVGFDQLLVV
60 70 80 90 100
EAPYDPESDF HYRIFNADGS EVEQCGNGAR CFARFVRMKG LTNKYTIHVS
110 120 130 140 150
TKKGKMVLNV EEEDLITVNM GVPEFEPNKI PFRAKQSEKT YILRVGEHTL
160 170 180 190 200
FCGAVSMGNP HVVTVVDDIR TAAVETLGPL LESHERFPER VNAGFMQVVS
210 220 230 240 250
RDEINLRVYE RGAGETQACG SGACAAVAVG ILQGLLDEQV RVHLPGGELE
260 270
IHWQGPGKPL YMTGPATHIY DGQISC
Length:276
Mass (Da):30,651
Last modified:June 6, 2002 - v2
Checksum:i8FCFEC10E5DD714B
GO

Sequence cautioni

The sequence AAF93303.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF93303.1. Different initiation.
PIRiG82360.
RefSeqiNP_229784.2. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF93303; AAF93303; VC_0126.
GeneIDi2614550.
KEGGivch:VC0126.
PATRICi20079296. VBIVibCho83274_0117.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF93303.1. Different initiation.
PIRiG82360.
RefSeqiNP_229784.2. NC_002505.1.

3D structure databases

ProteinModelPortaliQ9KVL6.
SMRiQ9KVL6. Positions 4-275.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243277.VC0126.

Protocols and materials databases

DNASUi2614550.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF93303; AAF93303; VC_0126.
GeneIDi2614550.
KEGGivch:VC0126.
PATRICi20079296. VBIVibCho83274_0117.

Phylogenomic databases

eggNOGiCOG0253.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

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: ATCC 39315 / El Tor Inaba N16961.

Entry informationi

Entry nameiDAPF_VIBCH
AccessioniPrimary (citable) accession number: Q9KVL6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 6, 2002
Last sequence update: June 6, 2002
Last modified: January 7, 2015
This is version 79 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.