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B2UD25

- DAPF_RALPJ

UniProt

B2UD25 - DAPF_RALPJ

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Ralstonia pickettii (strain 12J)
Status
Reviewed - 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 sitei166 – 1661SubstrateUniRule annotation
Sitei168 – 1681Important for catalytic activityUniRule annotation
Binding sitei199 – 1991SubstrateUniRule annotation
Sitei217 – 2171Important for catalytic activityUniRule annotation
Active sitei226 – 2261Proton 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

BioCyciRPIC402626:GH94-38-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:Rpic_0039
OrganismiRalstonia pickettii (strain 12J)
Taxonomic identifieri402626 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeRalstonia
ProteomesiUP000002566: Chromosome 1

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 292292Diaminopimelate epimerasePRO_1000099258Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 226

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi402626.Rpic_0039.

Structurei

3D structure databases

ProteinModelPortaliB2UD25.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni75 – 773Substrate bindingUniRule annotation
Regioni217 – 2182Substrate bindingUniRule annotation
Regioni227 – 2282Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLIVEPPY.
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.

B2UD25-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKLHFTKMHG AGNDFVVLDG IQTPIDFTPE QWAAIADRHF GVGADQLLLV
60 70 80 90 100
ERSTRPDVDF RYRIFNHDGG EVEHCGNGAR CFVKFVTDRG LTDKRTVRVE
110 120 130 140 150
VMNGIATLTM QDDGQVTVDM GAPVFEAARL PFLPEGLPTR TQGDDTQHAL
160 170 180 190 200
QINGRTEWLS TVSMGNPHAV QIVDDTEAFP VLEDGPLIES HAVFPRRVNA
210 220 230 240 250
GFMQIVDRHS VRLRVYERGA GETLACGTGA CAAVVAGIRR GLLDSPVKVA
260 270 280 290
THGGDLTIAW AGDGQPVMMT GPATTVFEGT LDLDALKLTA AH
Length:292
Mass (Da):31,627
Last modified:July 1, 2008 - v1
Checksum:iE26541341FCBA9E9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001068 Genomic DNA. Translation: ACD25204.1.
RefSeqiYP_001897636.1. NC_010682.1.

Genome annotation databases

EnsemblBacteriaiACD25204; ACD25204; Rpic_0039.
GeneIDi6289735.
KEGGirpi:Rpic_0039.
PATRICi20250934. VBIRalPic63053_1236.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001068 Genomic DNA. Translation: ACD25204.1 .
RefSeqi YP_001897636.1. NC_010682.1.

3D structure databases

ProteinModelPortali B2UD25.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 402626.Rpic_0039.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACD25204 ; ACD25204 ; Rpic_0039 .
GeneIDi 6289735.
KEGGi rpi:Rpic_0039.
PATRICi 20250934. VBIRalPic63053_1236.

Phylogenomic databases

eggNOGi COG0253.
HOGENOMi HOG000220466.
KOi K01778.
OMAi LIVEPPY.
OrthoDBi EOG6ND0M5.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci RPIC402626:GH94-38-MONOMER.

Family and domain databases

HAMAPi MF_00197. DAP_epimerase.
InterProi IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view ]
PANTHERi PTHR31689. PTHR31689. 1 hit.
Pfami PF01678. DAP_epimerase. 2 hits.
[Graphical view ]
TIGRFAMsi TIGR00652. DapF. 1 hit.
PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete sequence of chromosome 1 of Ralstonia pickettii 12J."
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Meincke L., Brettin T., Detter J.C., Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L.
    , Kyrpides N., Mikhailova N., Marsh T., Richardson P.
    Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 12J.

Entry informationi

Entry nameiDAPF_RALPJ
AccessioniPrimary (citable) accession number: B2UD25
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 1, 2008
Last modified: October 29, 2014
This is version 45 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