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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
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

Pathway: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei22 – 221SubstrateUniRule annotation
Binding sitei56 – 561SubstrateUniRule annotation
Binding sitei76 – 761SubstrateUniRule annotation
Active sitei85 – 851Proton 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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciBAPH224915:GJ9D-533-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:bbp_533
OrganismiBuchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
Taxonomic identifieri224915 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeBuchnera
ProteomesiUP000000601 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 – 286286Diaminopimelate epimerasePRO_0000149827Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi85 ↔ 229

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi224915.bbp533.

Structurei

3D structure databases

ProteinModelPortaliP59582.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni19 – 202Substrate bindingUniRule annotation
Regioni85 – 873Substrate bindingUniRule annotation
Regioni220 – 2212Substrate 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.

P59582-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHIKVVHKSV KIKFSKMHGL GNDFIIINAM MQKTFPVTSN IIQNLSNRYT
60 70 80 90 100
GIGFDQLLLV ENSKNVNIDF HYRIFNANGT EVSQCGNGAR CFALFVLLKK
110 120 130 140 150
LTKKRTLYVS TNTTTLILNV LNNGNVCVDM GVPCFKLKNI FGENIIENSL
160 170 180 190 200
HSIKFVNKII NYDLVSIGNP HCIIYVNNLK KYPVKKIGFY LSTHKIFPEG
210 220 230 240 250
INVNFVEVLS KNEIALRVYE RGVGETLACG SGACASVALG IQQGLLFNEV
260 270 280
QVNLLNGILK INWKGGSEKL YMTGPAVHVY DGYFYL
Length:286
Mass (Da):31,978
Last modified:April 11, 2003 - v1
Checksum:i9FB2231DDAD4E8A4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016826 Genomic DNA. Translation: AAO27235.1.
RefSeqiNP_778130.1. NC_004545.1.
WP_011091636.1. NC_004545.1.

Genome annotation databases

EnsemblBacteriaiAAO27235; AAO27235; bbp_533.
KEGGibab:bbp533.
PATRICi21245891. VBIBucAph80364_0530.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016826 Genomic DNA. Translation: AAO27235.1.
RefSeqiNP_778130.1. NC_004545.1.
WP_011091636.1. NC_004545.1.

3D structure databases

ProteinModelPortaliP59582.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224915.bbp533.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO27235; AAO27235; bbp_533.
KEGGibab:bbp533.
PATRICi21245891. VBIBucAph80364_0530.

Phylogenomic databases

eggNOGiCOG0253.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciBAPH224915:GJ9D-533-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: Bp.

Entry informationi

Entry nameiDAPF_BUCBP
AccessioniPrimary (citable) accession number: P59582
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 11, 2003
Last sequence update: April 11, 2003
Last modified: May 27, 2015
This is version 81 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.