EzCatDB: S00067
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DB codeS00067
CATH domainDomain 12.30.30.60 : SH3 type barrels.Catalytic domain
E.C.1.5.1.3
CSA1vie


Enzyme Name
UniProtKBKEGG

P00383
Protein nameDihydrofolate reductase type 2dihydrofolate reductase
tetrahydrofolate dehydrogenase
DHFR
pteridine reductase:dihydrofolate reductase
dihydrofolate reductase:thymidylate synthase
thymidylate synthetase-dihydrofolate reductase
folic acid reductase
folic reductase
dihydrofolic acid reductase
dihydrofolic reductase
7,8-dihydrofolate reductase
NADPH-dihydrofolate reductase
SynonymsEC 1.5.1.3
Dihydrofolate reductase type II
PfamPF06442 (DHFR_2)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00670One carbon pool by folate
MAP00790Folate biosynthesis

UniProtKB:Accession NumberP00383
Entry nameDYR21_ECOLX
Activity5,6,7,8-tetrahydrofolate + NADP(+) = 7,8- dihydrofolate + NADPH.
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00415C00005C00080C00101C00006
Compound7,8-DihydrofolateNADPHH+5,6,7,8-TetrahydrofolateNADP+
Typeamino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl groupamide group,amine group,nucleotideothersamino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl groupamide group,amine group,nucleotide
ChEBI15633
16474
15378
15635
20506
18009
PubChem98792
5884
1038
91443
5460413
5886
             
1vieAUnboundUnbound UnboundUnbound
1vifAAnalogue:FOLUnbound UnboundUnbound
2gqvAUnboundUnbound UnboundUnbound
2p4tAUnboundUnbound UnboundAnalogue:NAP
2rh2AUnboundUnbound UnboundUnbound
2rk1AAnalogue:DHFUnbound UnboundBound:NAP
2rk2AUnboundUnbound UnboundBound:NAP

Active-site residues
pdbMain-chain involved in catalysiscomment
          
1vieAILE 68
 
1vifAILE 68
 
2gqvAILE 68
 
2p4tAILE 68
mutant Q67H
2rh2AILE 68
 
2rk1AILE 68
 
2rk2AILE 68
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.4201-4202
[4]

[11]

[12]p.1048-1049
[13]

[16]p.14485-14486, Fig.7

references
[1]
PubMed ID3530319
JournalBiochemistry
Year1986
Volume25
Pages4194-204
AuthorsMatthews DA, Smith SL, Baccanari DP, Burchall JJ, Oatley SJ, Kraut J
TitleCrystal structure of a novel trimethoprim-resistant dihydrofolate reductase specified in Escherichia coli by R-plasmid R67.
[2]
PubMed ID1932013
JournalBiochemistry
Year1991
Volume30
Pages10895-904
AuthorsReece LJ, Nichols R, Ogden RC, Howell EE
TitleConstruction of a synthetic gene for an R-plasmid-encoded dihydrofolate reductase and studies on the role of the N-terminus in the protein.
[3]
PubMed ID8226776
JournalJ Biol Chem
Year1993
Volume268
Pages22672-9
AuthorsZhuang P, Yin M, Holland JC, Peterson CB, Howell EE
TitleArtificial duplication of the R67 dihydrofolate reductase gene to create protein asymmetry. Effects on protein activity and folding.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 17-78
Medline ID96069790
PubMed ID7583655
JournalNat Struct Biol
Year1995
Volume2
Pages1018-25
AuthorsNarayana N, Matthews DA, Howell EE, Nguyen-huu X
TitleA plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site.
Related PDB1vie,1vif
Related UniProtKBP00383
[5]
PubMed ID8784197
JournalBiochemistry
Year1996
Volume35
Pages11414-24
AuthorsBradrick TD, Beechem JM, Howell EE
TitleUnusual binding stoichiometries and cooperativity are observed during binary and ternary complex formation in the single active pore of R67 dihydrofolate reductase, a D2 symmetric protein.
[6]
PubMed ID8910413
JournalJ Biol Chem
Year1996
Volume271
Pages28031-7
AuthorsBradrick TD, Shattuck C, Strader MB, Wicker C, Eisenstein E, Howell EE
TitleRedesigning the quaternary structure of R67 dihydrofolate reductase. Creation of an active monomer from a tetrameric protein by quadruplication of the gene.
[7]
PubMed ID8999931
JournalJ Biol Chem
Year1997
Volume272
Pages2252-8
AuthorsPark H, Zhuang P, Nichols R, Howell EE
TitleMechanistic studies of R67 dihydrofolate reductase. Effects of pH and an H62C mutation.
[8]
PubMed ID9543003
JournalProtein Eng
Year1997
Volume10
Pages1415-24
AuthorsPark H, Bradrick TD, Howell EE
TitleA glutamine 67--> histidine mutation in homotetrameric R67 dihydrofolate reductase results in four mutations per single active site pore and causes substantial substrate and cofactor inhibition.
[9]
PubMed ID10964572
JournalJ Mol Biol
Year2000
Volume302
Pages235-50
AuthorsDam J, Rose T, Goldberg ME, Blondel A
TitleComplementation between dimeric mutants as a probe of dimer-dimer interactions in tetrameric dihydrofolate reductase encoded by R67 plasmid of E. coli.
[10]
PubMed ID11284680
JournalBiochemistry
Year2001
Volume40
Pages4242-52
AuthorsLi D, Levy LA, Gabel SA, Lebetkin MS, DeRose EF, Wall MJ, Howell EE, London RE
TitleInterligand Overhauser effects in type II dihydrofolate reductase.
[11]
PubMed ID11560482
JournalBiochemistry
Year2001
Volume40
Pages11344-52
AuthorsStrader MB, Smiley RD, Stinnett LG, VerBerkmoes NC, Howell EE
TitleRole of S65, Q67, I68, and Y69 residues in homotetrameric R67 dihydrofolate reductase.
[12]
PubMed ID11989624
JournalJ Comput Aided Mol Des
Year2001
Volume15
Pages1035-52
AuthorsHowell EE, Shukla U, Hicks SN, Smiley RD, Kuhn LA, Zavodszky MI
TitleOne site fits both: a model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme.
[13]
PubMed ID15812782
JournalChembiochem
Year2005
Volume6
Pages590-600
AuthorsHowell EE
TitleSearching sequence space: two different approaches to dihydrofolate reductase catalysis.
[14]
PubMed ID16790925
JournalActa Crystallogr D Biol Crystallogr
Year2006
Volume62
Pages695-706
AuthorsNarayana N
TitleHigh-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site.
Related PDB2gqv
[15]
PubMed ID17473013
JournalProtein Sci
Year2007
Volume16
Pages1063-8
AuthorsDivya N, Grifith E, Narayana N
TitleStructure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode.
Related PDB2p4t
[16]
PubMed ID18052202
JournalBiochemistry
Year2007
Volume46
Pages14878-88
AuthorsKrahn JM, Jackson MR, DeRose EF, Howell EE, London RE
TitleCrystal structure of a type II dihydrofolate reductase catalytic ternary complex.
Related PDB2rh2,2rk1,2rk2

comments
According to the literature [13], Lys32, Gln67, and Tyr69 have been reported to act as catalytic residues. However, they seem to contribute to the ligand binding, rather than catalysis (see [16]).
According to the literature [16], the reaction of this enzyme occurs in two steps: a hydride transfer from NADPH to the C6 atom of dihydrofolate (DHF), and a protonation step. The protonation step is more likely to preceed the hydride transfer step (see [16]), in general. However, no residues in close to the ligand seem to be involved in the protonation. On the other hand, the p-aminobenzoyl glutamate tail of DHF might be involved in substrate-assisted catalysis (see [16]). Its glutamate group might donate the proton to the N5 atom of DHF, to facilitate the reaction. In the next step, the hydride transfer may be assisted by the mainchain amide and carbonyl of Ile68 (see [16]).

createdupdated
2004-01-292009-03-17


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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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