EzCatDB: S00067

DB codeS00067
CATH domainDomain 12.30.30.60Catalytic domain
E.C.1.5.1.3
CSA1vie


Enzyme Name
Swiss-protKEGG

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

KEGG pathways
MAP codePathways
MAP00670One carbon pool by folate
MAP00790Folate biosynthesis

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


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
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 Swiss-protP00383
[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


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
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)

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