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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methylobacterium nodulans (strain ORS2060 / LMG 21967)
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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciMNOD460265:GCZK-184-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:Mnod_0183
OrganismiMethylobacterium nodulans (strain ORS2060 / LMG 21967)
Taxonomic identifieri460265 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesMethylobacteriaceaeMethylobacterium
ProteomesiUP000008207 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 – 293293Diaminopimelate epimerasePRO_1000124425Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi460265.Mnod_0183.

Structurei

3D structure databases

ProteinModelPortaliB8I9H6.
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.

B8I9H6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSPLAHRRFL KMNGLGNEIV VLDLRGTPHI VQPQEARAIA ADPRSRFDQL
60 70 80 90 100
MVLHDPVTAG TDAALRIYNT DGSESGACGN GTRCVAWAML EDPVMGRPAE
110 120 130 140 150
RLTLQSRAGL LAVTRVSATD FTVDMGPPRL RWDEIPLAEP FPDTRRIELQ
160 170 180 190 200
IGPIDDPILH SPGVVSMGNP HAVFFVDRDP ASYDLARIGP LLEAHPIFPE
210 220 230 240 250
RANISVAQVR GPEHIVLRVW ERGAGLTRAC GSAACAALVA AARLRLTGRR
260 270 280 290
AVVTLPGGDL VIDWGEDDHV RMTGPTELEW EGTLAPSLFA GAA
Length:293
Mass (Da):31,629
Last modified:March 3, 2009 - v1
Checksum:i8F57AA6895E459E4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001349 Genomic DNA. Translation: ACL55229.1.
RefSeqiWP_015926942.1. NC_011894.1.
YP_002495532.1. NC_011894.1.

Genome annotation databases

EnsemblBacteriaiACL55229; ACL55229; Mnod_0183.
KEGGimno:Mnod_0183.
PATRICi22542608. VBIMetNod76414_1055.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001349 Genomic DNA. Translation: ACL55229.1.
RefSeqiWP_015926942.1. NC_011894.1.
YP_002495532.1. NC_011894.1.

3D structure databases

ProteinModelPortaliB8I9H6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi460265.Mnod_0183.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL55229; ACL55229; Mnod_0183.
KEGGimno:Mnod_0183.
PATRICi22542608. VBIMetNod76414_1055.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiENHPMFP.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciMNOD460265:GCZK-184-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. "Complete sequence of chromosome of Methylobacterium nodulans ORS 2060."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ORS2060 / LMG 21967.

Entry informationi

Entry nameiDAPF_METNO
AccessioniPrimary (citable) accession number: B8I9H6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 3, 2009
Last modified: May 27, 2015
This is version 43 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.