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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methylobacterium sp. (strain 4-46)
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 sitei17 – 171SubstrateUniRule annotation
Binding sitei49 – 491SubstrateUniRule annotation
Binding sitei69 – 691SubstrateUniRule annotation
Active sitei78 – 781Proton donor/acceptorUniRule annotation
Binding sitei169 – 1691SubstrateUniRule annotation
Sitei171 – 1711Important for catalytic activityUniRule annotation
Binding sitei203 – 2031SubstrateUniRule annotation
Sitei221 – 2211Important for catalytic activityUniRule annotation
Active sitei230 – 2301Proton 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

BioCyciMSP426117:GI2I-3692-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:M446_3656
OrganismiMethylobacterium sp. (strain 4-46)
Taxonomic identifieri426117 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesMethylobacteriaceaeMethylobacterium
ProteomesiUP000001185: 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 – 293293Diaminopimelate epimerasePRO_1000099247Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi78 ↔ 230

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi426117.M446_3656.

Structurei

3D structure databases

ProteinModelPortaliB0UCI8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 152Substrate bindingUniRule annotation
Regioni78 – 803Substrate bindingUniRule annotation
Regioni221 – 2222Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiENHPMFP.
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.

B0UCI8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSPLADHRFL KMNGLGNEIV VLDLRASSHV VRPEEARAIA ADPRSRFDQL
60 70 80 90 100
MVLHDPVTPG TDARLRIYNR DGSESGACGN GTRCVAWAMR ADPVMGRAGE
110 120 130 140 150
QLTLESAAGL LAVTRVSDTD FTVDMGPPHL RWDEIPLSEP FPDTRRIELQ
160 170 180 190 200
IGPIDAPILH SPGVVSMGNP HAVFFVDRDP ETYDLGRIGP LLEAHPLFPE
210 220 230 240 250
RANISLAQVV AADRIRLRVW ERGAGLTRAC GSAACAALVA AARLRLTGRR
260 270 280 290
ATVTLPGGDL VIAWGEDDHV RMTGPTELEW EGRFPPALFA GAA
Length:293
Mass (Da):31,711
Last modified:April 8, 2008 - v1
Checksum:iFC67809E27D0582A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000943 Genomic DNA. Translation: ACA18037.1.
RefSeqiWP_012333436.1. NC_010511.1.
YP_001770471.1. NC_010511.1.

Genome annotation databases

EnsemblBacteriaiACA18037; ACA18037; M446_3656.
GeneIDi6132645.
KEGGimet:M446_3656.
PATRICi22588571. VBIMetSp32184_3625.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000943 Genomic DNA. Translation: ACA18037.1.
RefSeqiWP_012333436.1. NC_010511.1.
YP_001770471.1. NC_010511.1.

3D structure databases

ProteinModelPortaliB0UCI8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi426117.M446_3656.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACA18037; ACA18037; M446_3656.
GeneIDi6132645.
KEGGimet:M446_3656.
PATRICi22588571. VBIMetSp32184_3625.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiENHPMFP.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciMSP426117:GI2I-3692-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: 4-46.

Entry informationi

Entry nameiDAPF_METS4
AccessioniPrimary (citable) accession number: B0UCI8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 8, 2008
Last modified: January 7, 2015
This is version 52 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.