DB code: S00067

CATH domain 2.30.30.60 : SH3 type barrels. Catalytic domain
E.C. 1.5.1.3
CSA 1vie
M-CSA 1vie
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P00383 Dihydrofolate reductase type 2
EC 1.5.1.3
Dihydrofolate reductase type II
PF06442 (DHFR_2)
[Graphical View]

KEGG enzyme name
dihydrofolate 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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00383 DYR21_ECOLX 5,6,7,8-tetrahydrofolate + NADP(+) = 7,8- dihydrofolate + NADPH.

KEGG Pathways
Map code Pathways E.C.
MAP00790 Folate biosynthesis
MAP00670 One carbon pool by folate

Compound table
Substrates Products Intermediates
KEGG-id C00415 C00005 C00080 C00101 C00006
E.C.
Compound 7,8-Dihydrofolate NADPH H+ 5,6,7,8-Tetrahydrofolate NADP+
Type amino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl group amide group,amine group,nucleotide others amino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl group amide group,amine group,nucleotide
ChEBI 15633
16474
15378
15635
20506
18009
PubChem 98792
5884
1038
5460413
91443
5886
1vieA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1vifA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:FOL Unbound Unbound Unbound
2gqvA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2p4tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:NAP
2rh2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2rk1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DHF Unbound Unbound Bound:NAP
2rk2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1vieA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ILE 68
1vifA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ILE 68
2gqvA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ILE 68
2p4tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ILE 68 mutant Q67H
2rh2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ILE 68
2rk1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ILE 68
2rk2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ILE 68

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.4201-4202
[4]
[11]
[12]
p.1048-1049
[13]
[16]
p.14485-14486, Fig.7

References
[1]
Resource
Comments
Medline ID
PubMed ID 3530319
Journal Biochemistry
Year 1986
Volume 25
Pages 4194-204
Authors Matthews DA, Smith SL, Baccanari DP, Burchall JJ, Oatley SJ, Kraut J
Title Crystal structure of a novel trimethoprim-resistant dihydrofolate reductase specified in Escherichia coli by R-plasmid R67.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1932013
Journal Biochemistry
Year 1991
Volume 30
Pages 10895-904
Authors Reece LJ, Nichols R, Ogden RC, Howell EE
Title Construction of a synthetic gene for an R-plasmid-encoded dihydrofolate reductase and studies on the role of the N-terminus in the protein.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8226776
Journal J Biol Chem
Year 1993
Volume 268
Pages 22672-9
Authors Zhuang P, Yin M, Holland JC, Peterson CB, Howell EE
Title Artificial duplication of the R67 dihydrofolate reductase gene to create protein asymmetry. Effects on protein activity and folding.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 17-78
Medline ID 96069790
PubMed ID 7583655
Journal Nat Struct Biol
Year 1995
Volume 2
Pages 1018-25
Authors Narayana N, Matthews DA, Howell EE, Nguyen-huu X
Title A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site.
Related PDB 1vie 1vif
Related UniProtKB P00383
[5]
Resource
Comments
Medline ID
PubMed ID 8784197
Journal Biochemistry
Year 1996
Volume 35
Pages 11414-24
Authors Bradrick TD, Beechem JM, Howell EE
Title Unusual 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.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8910413
Journal J Biol Chem
Year 1996
Volume 271
Pages 28031-7
Authors Bradrick TD, Shattuck C, Strader MB, Wicker C, Eisenstein E, Howell EE
Title Redesigning the quaternary structure of R67 dihydrofolate reductase. Creation of an active monomer from a tetrameric protein by quadruplication of the gene.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 8999931
Journal J Biol Chem
Year 1997
Volume 272
Pages 2252-8
Authors Park H, Zhuang P, Nichols R, Howell EE
Title Mechanistic studies of R67 dihydrofolate reductase. Effects of pH and an H62C mutation.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9543003
Journal Protein Eng
Year 1997
Volume 10
Pages 1415-24
Authors Park H, Bradrick TD, Howell EE
Title A 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.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10964572
Journal J Mol Biol
Year 2000
Volume 302
Pages 235-50
Authors Dam J, Rose T, Goldberg ME, Blondel A
Title Complementation between dimeric mutants as a probe of dimer-dimer interactions in tetrameric dihydrofolate reductase encoded by R67 plasmid of E. coli.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 11284680
Journal Biochemistry
Year 2001
Volume 40
Pages 4242-52
Authors Li D, Levy LA, Gabel SA, Lebetkin MS, DeRose EF, Wall MJ, Howell EE, London RE
Title Interligand Overhauser effects in type II dihydrofolate reductase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11560482
Journal Biochemistry
Year 2001
Volume 40
Pages 11344-52
Authors Strader MB, Smiley RD, Stinnett LG, VerBerkmoes NC, Howell EE
Title Role of S65, Q67, I68, and Y69 residues in homotetrameric R67 dihydrofolate reductase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11989624
Journal J Comput Aided Mol Des
Year 2001
Volume 15
Pages 1035-52
Authors Howell EE, Shukla U, Hicks SN, Smiley RD, Kuhn LA, Zavodszky MI
Title One site fits both: a model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 15812782
Journal Chembiochem
Year 2005
Volume 6
Pages 590-600
Authors Howell EE
Title Searching sequence space: two different approaches to dihydrofolate reductase catalysis.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 16790925
Journal Acta Crystallogr D Biol Crystallogr
Year 2006
Volume 62
Pages 695-706
Authors Narayana N
Title High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site.
Related PDB 2gqv
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 17473013
Journal Protein Sci
Year 2007
Volume 16
Pages 1063-8
Authors Divya N, Grifith E, Narayana N
Title Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode.
Related PDB 2p4t
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 18052202
Journal Biochemistry
Year 2007
Volume 46
Pages 14878-88
Authors Krahn JM, Jackson MR, DeRose EF, Howell EE, London RE
Title Crystal structure of a type II dihydrofolate reductase catalytic ternary complex.
Related PDB 2rh2 2rk1 2rk2
Related UniProtKB

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]).

Created Updated
2004-01-29 2009-03-17