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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Prochlorococcus marinus (strain MIT 9313)
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 sitei15 – 151SubstrateUniRule annotation
Binding sitei53 – 531SubstrateUniRule annotation
Binding sitei72 – 721SubstrateUniRule annotation
Active sitei81 – 811Proton donor/acceptorUniRule annotation
Binding sitei169 – 1691SubstrateUniRule annotation
Sitei171 – 1711Important for catalytic activityUniRule annotation
Binding sitei202 – 2021SubstrateUniRule annotation
Sitei220 – 2201Important for catalytic activityUniRule annotation
Active sitei229 – 2291Proton 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

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:PMT_0716
OrganismiProchlorococcus marinus (strain MIT 9313)
Taxonomic identifieri74547 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaProchloralesProchlorococcaceaeProchlorococcus
ProteomesiUP000001423 Componenti: Chromosome

Subcellular locationi

  1. 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 – 303303Diaminopimelate epimerasePRO_1000077701Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi81 ↔ 229

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi74547.PMT0716.

Structurei

3D structure databases

ProteinModelPortaliQ7V7M5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni12 – 132Substrate bindingUniRule annotation
Regioni81 – 833Substrate bindingUniRule annotation
Regioni220 – 2212Substrate bindingUniRule annotation
Regioni230 – 2312Substrate 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.

Q7V7M5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLVMLQFSKY QGLGNDFLLI DGREDQLTQQ VINPDPAWVR KICDRHFGIG
60 70 80 90 100
ADGLILALPP RADGDLRMQI FNADGSLAEM CGNGIRCLTR FLADIEGDLC
110 120 130 140 150
VQRWNIETLA GIICPVLQED GQICVDMGTP FLDPESIPTT LTIGSAGLPQ
160 170 180 190 200
GECHLGSTSL HVAAVGMGNP HLIVPVEDLE NIPFENWGQR LEKHHAFPAK
210 220 230 240 250
TNVHFLKIHS PNQLEIRVWE RGSGPTLACG TGACASLVAT CLLGLSDDHA
260 270 280 290 300
EVLLPGGVLQ ISWPGRRGSV FMTGPAEPIF DGVLTPLLSP SHAEVLPQDD

QII
Length:303
Mass (Da):32,747
Last modified:October 1, 2003 - v1
Checksum:i55D2D70E12958C9E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX548175 Genomic DNA. Translation: CAE20891.1.
RefSeqiNP_894548.1. NC_005071.1.
WP_011130094.1. NC_005071.1.

Genome annotation databases

EnsemblBacteriaiCAE20891; CAE20891; PMT_0716.
KEGGipmt:PMT0716.
PATRICi23009409. VBIProMar135351_0859.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX548175 Genomic DNA. Translation: CAE20891.1.
RefSeqiNP_894548.1. NC_005071.1.
WP_011130094.1. NC_005071.1.

3D structure databases

ProteinModelPortaliQ7V7M5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi74547.PMT0716.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAE20891; CAE20891; PMT_0716.
KEGGipmt:PMT0716.
PATRICi23009409. VBIProMar135351_0859.

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: MIT 9313.

Entry informationi

Entry nameiDAPF_PROMM
AccessioniPrimary (citable) accession number: Q7V7M5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: October 1, 2003
Last modified: April 29, 2015
This is version 77 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.