UniProtKB - P0A6K1 (DAPF_ECOLI)
Protein
Diaminopimelate epimerase
Gene
dapF
Organism
Escherichia coli (strain K12)
Status
Functioni
Involved in the succinylase branch of the L-lysine biosynthesis and in the biosynthesis of the pentapeptide incorporated in the peptidoglycan moiety (PubMed:3283102). Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP) (PubMed:6378903, PubMed:3031013, PubMed:3042781).4 Publications
Miscellaneous
DapF utilizes a two-base mechanism involving a pair of cysteine residues (Cys-73 and Cys-217).1 Publication
Catalytic activityi
- EC:5.1.1.72 Publications
Activity regulationi
Inhibited by 2-(4-amino-4-carboxybutyl)aziri-dine-2-carboxylate (aziDAP) and iodoacetamide.3 Publications
Kineticsi
- KM=0.16 mM for D,L-DAP (at pH 7.8 and at 25 degrees Celsius)2 Publications
- KM=0.26 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)2 Publications
- KM=0.36 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)2 Publications
: L-lysine biosynthesis via DAP pathway Pathwayi
This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.1 PublicationProteins known to be involved in this subpathway in this organism are:
- Diaminopimelate epimerase (dapF), Diaminopimelate epimerase (dapF)
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 11 | SubstrateUniRule annotation | 1 | |
Binding sitei | 44 | SubstrateUniRule annotation | 1 | |
Binding sitei | 64 | SubstrateUniRule annotation | 1 | |
Active sitei | 73 | Proton donorUniRule annotation | 1 | |
Binding sitei | 157 | SubstrateUniRule annotation | 1 | |
Sitei | 159 | Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation | 1 | |
Binding sitei | 190 | SubstrateUniRule annotation | 1 | |
Sitei | 208 | Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation | 1 | |
Active sitei | 217 | Proton acceptorUniRule annotation | 1 | |
Sitei | 268 | Important for dimerization1 Publication | 1 |
GO - Molecular functioni
- diaminopimelate epimerase activity Source: EcoCyc
GO - Biological processi
- lysine biosynthetic process via diaminopimelate Source: GO_Central
Keywordsi
Molecular function | Isomerase |
Biological process | Amino-acid biosynthesis, Lysine biosynthesis |
Enzyme and pathway databases
BioCyci | EcoCyc:DIAMINOPIMEPIM-MONOMER MetaCyc:DIAMINOPIMEPIM-MONOMER |
UniPathwayi | UPA00034;UER00025 |
Names & Taxonomyi
Protein namesi | Recommended name: Diaminopimelate epimerase1 Publication (EC:5.1.1.72 Publications)Short name: DAP epimerase1 Publication Alternative name(s): PLP-independent amino acid racemaseUniRule annotation |
Gene namesi | Name:dapF1 Publication Ordered Locus Names:b3809, JW5592 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
- Cytoplasm Curated
GO - Cellular componenti
- cytosol Source: EcoCyc
Keywords - Cellular componenti
CytoplasmPathology & Biotechi
Disruption phenotypei
Cells lacking this gene show an unusual large LL-diaminopimelic acid (LL-DAP) pool and an important variations of the LL-DAP/meso-DAP ratio incorporated in the peptidoglycan.1 Publication
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 268 | Y → A: Significantly less active than the wild-type dimer and unable to dimerize. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000149838 | 1 – 274 | Diaminopimelate epimeraseAdd BLAST | 274 |
Proteomic databases
jPOSTi | P0A6K1 |
PaxDbi | P0A6K1 |
PRIDEi | P0A6K1 |
Interactioni
Subunit structurei
Homodimer.
2 PublicationsProtein-protein interaction databases
BioGRIDi | 4263254, 9 interactors |
DIPi | DIP-47856N |
IntActi | P0A6K1, 2 interactors |
STRINGi | 511145.b3809 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P0A6K1 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 74 – 75 | Substrate bindingUniRule annotation | 2 | |
Regioni | 208 – 209 | Substrate bindingUniRule annotation | 2 | |
Regioni | 218 – 219 | Substrate bindingUniRule annotation | 2 |
Sequence similaritiesi
Belongs to the diaminopimelate epimerase family.Curated
Phylogenomic databases
eggNOGi | COG0253, Bacteria |
HOGENOMi | CLU_053306_1_1_6 |
InParanoidi | P0A6K1 |
PhylomeDBi | P0A6K1 |
Family and domain databases
HAMAPi | MF_00197, DAP_epimerase, 1 hit |
InterProi | View protein in InterPro IPR018510, DAP_epimerase_AS IPR001653, DAP_epimerase_DapF |
PANTHERi | PTHR31689, PTHR31689, 1 hit |
Pfami | View protein in Pfam PF01678, DAP_epimerase, 2 hits |
TIGRFAMsi | TIGR00652, DapF, 1 hit |
PROSITEi | View protein in PROSITE PS01326, DAP_EPIMERASE, 1 hit |
i Sequence
Sequence statusi: Complete.
P0A6K1-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MQFSKMHGLG NDFMVVDAVT QNVFFSPELI RRLADRHLGV GFDQLLVVEP
60 70 80 90 100
PYDPELDFHY RIFNADGSEV AQCGNGARCF ARFVRLKGLT NKRDIRVSTA
110 120 130 140 150
NGRMVLTVTD DDLVRVNMGE PNFEPSAVPF RANKAEKTYI MRAAEQTILC
160 170 180 190 200
GVVSMGNPHC VIQVDDVDTA AVETLGPVLE SHERFPERAN IGFMQVVKRE
210 220 230 240 250
HIRLRVYERG AGETQACGSG ACAAVAVGIQ QGLLAEEVRV ELPGGRLDIA
260 270
WKGPGHPLYM TGPAVHVYDG FIHL
Sequence cautioni
The sequence AAA67605 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated
The sequence CAA31413 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 98 | S → T in CAA31413 (PubMed:3057443).Curated | 1 | |
Sequence conflicti | 160 – 161 | CV → WL in CAA31413 (PubMed:3057443).Curated | 2 | |
Sequence conflicti | 200 – 201 | EH → DD in CAA31413 (PubMed:3057443).Curated | 2 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X12968 Genomic DNA Translation: CAA31413.1 Different initiation. M87049 Genomic DNA Translation: AAA67605.1 Different initiation. U00096 Genomic DNA Translation: AAC76812.2 AP009048 Genomic DNA Translation: BAE77491.1 M38257 Genomic DNA Translation: AAA24761.1 X66782 Genomic DNA Translation: CAA47282.1 |
PIRi | B65185, S01913 |
RefSeqi | NP_418254.2, NC_000913.3 WP_001160654.1, NZ_STEB01000021.1 |
Genome annotation databases
EnsemblBacteriai | AAC76812; AAC76812; b3809 BAE77491; BAE77491; BAE77491 |
GeneIDi | 58349181 948364 |
KEGGi | ecj:JW5592 eco:b3809 |
PATRICi | fig|511145.12.peg.3925 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X12968 Genomic DNA Translation: CAA31413.1 Different initiation. M87049 Genomic DNA Translation: AAA67605.1 Different initiation. U00096 Genomic DNA Translation: AAC76812.2 AP009048 Genomic DNA Translation: BAE77491.1 M38257 Genomic DNA Translation: AAA24761.1 X66782 Genomic DNA Translation: CAA47282.1 |
PIRi | B65185, S01913 |
RefSeqi | NP_418254.2, NC_000913.3 WP_001160654.1, NZ_STEB01000021.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
4IJZ | X-ray | 2.00 | A/B | 1-274 | [»] | |
4IK0 | X-ray | 2.05 | A/B | 1-274 | [»] | |
5YGU | X-ray | 2.30 | A | 1-274 | [»] | |
6VCK | X-ray | 2.69 | A | 1-274 | [»] | |
6VCL | X-ray | 2.06 | A | 1-274 | [»] | |
6VCM | X-ray | 2.35 | A | 1-274 | [»] | |
SMRi | P0A6K1 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4263254, 9 interactors |
DIPi | DIP-47856N |
IntActi | P0A6K1, 2 interactors |
STRINGi | 511145.b3809 |
Proteomic databases
jPOSTi | P0A6K1 |
PaxDbi | P0A6K1 |
PRIDEi | P0A6K1 |
Genome annotation databases
EnsemblBacteriai | AAC76812; AAC76812; b3809 BAE77491; BAE77491; BAE77491 |
GeneIDi | 58349181 948364 |
KEGGi | ecj:JW5592 eco:b3809 |
PATRICi | fig|511145.12.peg.3925 |
Organism-specific databases
EchoBASEi | EB0205 |
Phylogenomic databases
eggNOGi | COG0253, Bacteria |
HOGENOMi | CLU_053306_1_1_6 |
InParanoidi | P0A6K1 |
PhylomeDBi | P0A6K1 |
Enzyme and pathway databases
UniPathwayi | UPA00034;UER00025 |
BioCyci | EcoCyc:DIAMINOPIMEPIM-MONOMER MetaCyc:DIAMINOPIMEPIM-MONOMER |
Miscellaneous databases
PROi | PR:P0A6K1 |
Family and domain databases
HAMAPi | MF_00197, DAP_epimerase, 1 hit |
InterProi | View protein in InterPro IPR018510, DAP_epimerase_AS IPR001653, DAP_epimerase_DapF |
PANTHERi | PTHR31689, PTHR31689, 1 hit |
Pfami | View protein in Pfam PF01678, DAP_epimerase, 2 hits |
TIGRFAMsi | TIGR00652, DapF, 1 hit |
PROSITEi | View protein in PROSITE PS01326, DAP_EPIMERASE, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | DAPF_ECOLI | |
Accessioni | P0A6K1Primary (citable) accession number: P0A6K1 Secondary accession number(s): P08885 Q8X8P8 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | March 29, 2005 |
Last sequence update: | March 29, 2005 | |
Last modified: | February 10, 2021 | |
This is version 127 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PATHWAY comments
Index of metabolic and biosynthesis pathways - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families