P0ABQ4 (DYR_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Dihydrofolate reductase
EC=1.5.1.3

Gene names

Name:	folA
Synonyms:	tmrA
Ordered Locus Names:	b0048, JW0047

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	159 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
Catalytic activity	5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH. Ref.16
Pathway	Cofactor biosynthesis; tetrahydrofolate biosynthesis; 5,6,7,8-tetrahydrofolate from 7,8-dihydrofolate: step 1/1.
Miscellaneous	The strain K12 sequence is shown. Strain B [RT500] is resistant to 500 micrograms per milliliter of trimethoprim. Strain B [MB1428] is methotrexate-resistant.
Sequence similarities	Belongs to the dihydrofolate reductase family. Contains 1 DHFR (dihydrofolate reductase) domain.

Ontologies

Keywords
Biological process	Antibiotic resistance Methotrexate resistance One-carbon metabolism Trimethoprim resistance
Ligand	NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	10-formyltetrahydrofolate biosynthetic process Inferred from genetic interaction PubMed 2838456. Source: EcoCyc folic acid biosynthetic process Inferred from genetic interaction PubMed 2838456. Source: EcoCyc glycine biosynthetic process Inferred from electronic annotation. Source: InterPro nucleotide biosynthetic process Inferred from electronic annotation. Source: InterPro one-carbon metabolic process Inferred from electronic annotation. Source: UniProtKB-KW response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW response to drug Inferred from direct assay PubMed 6444603. Source: EcoliWiki response to methotrexate Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	NADP binding Inferred from electronic annotation. Source: InterPro dihydrofolate reductase activity Inferred from direct assay PubMed 46. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 159

159

Dihydrofolate reductase

PRO_0000186387

Regions

Domain

1 – 158

158

DHFR

Nucleotide binding

13 – 19

7

NADP

Nucleotide binding

45 – 46

2

NADP

Nucleotide binding

63 – 64

2

NADP

Nucleotide binding

95 – 102

8

NADP

Sites

Binding site

5

1

Substrate; via carbonyl oxygen

Binding site

7

1

NADP; via amide nitrogen and carbonyl oxygen

Binding site

27

1

Substrate

Binding site

52

1

Substrate

Binding site

57

1

Substrate

Binding site

76

1

NADP; via carbonyl oxygen

Binding site

113

1

Substrate

Natural variations

Natural variant

28

1

L → R in strain: B[RT500] isozyme 2.

Natural variant

30

1

W → G in strain: 1810.

Natural variant

154

1

E → K in strain: B[MB1428].

Natural variant

154

1

E → Q in strain: 1810.

Experimental info

Mutagenesis

16

1

M → F or S: Increases catalytic rate about 2-fold. Ref.16

Mutagenesis

16

1

M → N: Increases catalytic rate about 2-fold. Increases catalytic rate about 7-fold; when associated with L-20; Y-42; F-92; A-85 and S-152. Ref.16

Mutagenesis

20

1

M → I or V: Increases catalytic rate 2-fold. Ref.16

Mutagenesis

20

1

M → L: Increases catalytic rate 2.5-fold. Increases catalytic rate about 7-fold; when associated with N-16; Y-42; F-92; A-85 and S-152. Ref.16

Mutagenesis

42

1

M → V: Increases catalytic rate almost 2-fold. Ref.16

Mutagenesis

42

1

M → Y: Increases catalytic rate almost 2-fold. Increases catalytic rate about 7-fold; when associated with N-16; L-20; A-85; F-92 and S-152. Ref.16

Mutagenesis

85

1

C → A: Decreases catalytic rate by one third. Increases catalytic rate about 7-fold; when associated with N-16; L-20; Y-42; F-92 and S-152. Ref.16

Mutagenesis

92

1

M → F: No effect. Increases catalytic rate about 7-fold; when associated with N-16; L-20; Y-42; A-85 and S-152. Ref.16

Mutagenesis

92

1

M → L: No effect. Ref.16

Mutagenesis

152

1

C → S: Increases catalytic rate 1.5-fold. Increases catalytic rate about 7-fold; when associated with N-16; L-20; Y-42; A-85 and F-92. Ref.16

Secondary structure

1

.

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159

Helix Strand Turn

Details...

Beta strand

2 – 8

7

Helix

10 – 12

3

Beta strand

13 – 16

4

Helix

17 – 19

3

Helix

25 – 35

11

Beta strand

40 – 43

4

Helix

44 – 50

7

Beta strand

55 – 57

3

Beta strand

59 – 62

4

Beta strand

72 – 77

6

Helix

78 – 83

6

Turn

84 – 87

4

Beta strand

91 – 93

3

Helix

97 – 103

7

Helix

104 – 106

3

Beta strand

108 – 115

8

Beta strand

122 – 124

3

Helix

130 – 132

3

Beta strand

133 – 141

9

Beta strand

147 – 149

3

Beta strand

151 – 158

8

Sequences

	Sequence		Length	Mass (Da)
	P0ABQ4 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 6A03CDCD7F5F8562	FASTA	159	17,999
	10 20 30 40 50 60 MISLIAALAV DRVIGMENAM PWNLPADLAW FKRNTLNKPV IMGRHTWESI GRPLPGRKNI 70 80 90 100 110 120 ILSSQPGTDD RVTWVKSVDE AIAACGDVPE IMVIGGGRVY EQFLPKAQKL YLTHIDAEVE 130 140 150 GDTHFPDYEP DDWESVFSEF HDADAQNSHS YCFEILERR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The amino-acid sequence of the dihydrofolate reductase of a trimethoprim-resistant strain of Escherichia coli." Stone D., Phillips A.W., Burchall J.J. Eur. J. Biochem. 72:613-624(1977) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE (ISOZYME 1). Strain: B [RT500].
[2]	"Dihydrofolate reductase: the amino acid sequence of the enzyme from a methotrexate-resistant mutant of Escherichia coli." Bennett C.D., Rodkey J.A., Sondey J.M., Hirschmann R. Biochemistry 17:1328-1337(1978) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE. Strain: B [MB1428].
[3]	"Nucleotide sequence of the E coli gene coding for dihydrofolate reductase." Smith D.R., Calvo J.M. Nucleic Acids Res. 8:2255-2274(1980) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[4]	"Effect of a single amino acid substitution on Escherichia coli dihydrofolate reductase catalysis and ligand binding." Baccanari D.P., Stone D., Kuyper L. J. Biol. Chem. 256:1738-1747(1981) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE (ISOZYME 2). Strain: B [RT500].
[5]	"Massive overproduction of dihydrofolate reductase in bacteria as a response to the use of trimethoprim." Flensburg J., Skoeld O. Eur. J. Biochem. 162:473-476(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 1810.
[6]	"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region." Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[7]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[8]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[9]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[10]	"Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7-A resolution. II. Environment of bound NADPH and implications for catalysis." Filman D.J., Bolin J.T., Matthews D.A., Kraut J. J. Biol. Chem. 257:13663-13672(1982) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
[11]	"Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state." Bystroff C., Oatley S.J., Kraut J. Biochemistry 29:3263-3277(1990) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
[12]	"Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding." Bystroff C., Kraut J. Biochemistry 30:2227-2239(1991) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[13]	"Isomorphous crystal structures of Escherichia coli dihydrofolate reductase complexed with folate, 5-deazafolate, and 5,10-dideazatetrahydrofolate: mechanistic implications." Reyes V.M., Sawaya M.R., Brown K.A., Kraut J. Biochemistry 34:2710-2723(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEXES WITH NADPH; FOLATE; 5-DEAZAFOLATE AND 5,10-DIDEAZATETRAHYDROFOLATE.
[14]	"Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4." Lee H., Reyes V.M., Kraut J. Biochemistry 35:7012-7020(1996) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH 5-FORMYLTETRAHYDROFOLATE.
[15]	"Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence." Sawaya M.R., Kraut J. Biochemistry 36:586-603(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEXES WITH NADPH; METHOTREXATE AND TETRAHYDROFOLATE.
[16]	"Evolutional design of a hyperactive cysteine- and methionine-free mutant of Escherichia coli dihydrofolate reductase." Iwakura M., Maki K., Takahashi H., Takenawa T., Yokota A., Katayanagi K., Kamiyama T., Gekko K. J. Biol. Chem. 281:13234-13246(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH FOLATE, MASS SPECTROMETRY, CATALYTIC ACTIVITY, MUTAGENESIS OF MET-16; MET-20; MET-42; CYS-85; MET-92 AND CYS-152.
[17]	"A 2.13 A structure of E. coli dihydrofolate reductase bound to a novel competitive inhibitor reveals a new binding surface involving the M20 loop region." Summerfield R.L., Daigle D.M., Mayer S., Mallik D., Hughes D.W., Jackson S.G., Sulek M., Organ M.G., Brown E.D., Junop M.S. J. Med. Chem. 49:6977-6986(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.13 ANGSTROMS).
[18]	"Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate." Bennett B., Langan P., Coates L., Mustyakimov M., Schoenborn B., Howell E.E., Dealwis C. Proc. Natl. Acad. Sci. U.S.A. 103:18493-18498(2006) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NEUTRON DIFFRACTION (2.20 ANGSTROMS) IN COMPLEX WITH METHOTREXATE.
[19]	"X-ray structure of the ternary MTX.NADPH complex of the anthrax dihydrofolate reductase: a pharmacophore for dual-site inhibitor design." Bennett B.C., Wan Q., Ahmad M.F., Langan P., Dealwis C.G. J. Struct. Biol. 166:162-171(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH METHOTREXATE AND NADPH.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J01609 Genomic DNA. Translation: AAA87976.1.
X05108 Genomic DNA. Translation: CAA28755.1.
U00096 Genomic DNA. Translation: AAC73159.1.
AP009048 Genomic DNA. Translation: BAB96616.1.

PIR

RDECD. A93704.

RefSeq

NP_414590.1. NC_000913.2.
YP_488354.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DDR	X-ray	2.45	A/B	1-159	[»]
1DDS	X-ray	2.20	A/B	1-159	[»]
1DHI	X-ray	1.90	A/B	1-159	[»]
1DHJ	X-ray	1.80	A/B	1-159	[»]
1DRA	X-ray	1.90	A/B	1-159	[»]
1DRB	X-ray	1.96	A/B	1-159	[»]
1DRE	X-ray	2.60	A	1-159	[»]
1DRH	X-ray	2.30	A	1-159	[»]
1DYH	X-ray	1.90	A/B	1-159	[»]
1DYI	X-ray	1.90	A/B	1-159	[»]
1DYJ	X-ray	1.85	A/B	1-159	[»]
1JOL	X-ray	1.96	A/B	1-159	[»]
1JOM	X-ray	1.90	A	1-159	[»]
1RA1	X-ray	1.90	A	1-159	[»]
1RA2	X-ray	1.60	A	1-159	[»]
1RA3	X-ray	1.80	A	1-159	[»]
1RA8	X-ray	1.80	A	1-159	[»]
1RA9	X-ray	1.55	A	1-159	[»]
1RB2	X-ray	2.10	A/B	1-159	[»]
1RB3	X-ray	2.30	A/B	1-159	[»]
1RC4	X-ray	1.90	A	1-159	[»]
1RD7	X-ray	2.60	A/B	1-159	[»]
1RE7	X-ray	2.60	A/B	1-159	[»]
1RF7	X-ray	1.80	A	1-159	[»]
1RG7	X-ray	2.00	A	1-159	[»]
1RH3	X-ray	2.40	A	1-159	[»]
1RX1	X-ray	2.00	A	1-159	[»]
1RX2	X-ray	1.80	A	1-159	[»]
1RX3	X-ray	2.20	A	1-159	[»]
1RX4	X-ray	2.20	A	1-159	[»]
1RX5	X-ray	2.30	A	1-159	[»]
1RX6	X-ray	2.00	A	1-159	[»]
1RX7	X-ray	2.30	A	1-159	[»]
1RX8	X-ray	2.80	A	1-159	[»]
1RX9	X-ray	1.90	A	1-159	[»]
1TDR	X-ray	2.50	A/B	1-159	[»]
2ANO	X-ray	2.68	A	1-159	[»]
2ANQ	X-ray	2.13	A	1-159	[»]
2D0K	X-ray	1.90	A/B	2-159	[»]
2DRC	X-ray	1.90	A/B	1-159	[»]
2INQ	neutron diffraction	2.20	A/B	1-159	[»]
3DAU	X-ray	1.50	A	1-159	[»]
3DRC	X-ray	1.90	A/B	1-159	[»]
3K74	X-ray	1.95	A	1-159	[»]
3KFY	X-ray	2.08	A	1-159	[»]
3OCH	X-ray	1.79	A/B	1-159	[»]
3QL3	X-ray	1.80	A	1-159	[»]
3QYL	X-ray	1.79	A	1-159	[»]
3QYO	X-ray	2.09	A	1-159	[»]
3R33	X-ray	2.09	A	1-159	[»]
4DFR	X-ray	1.70	A/B	1-159	[»]
5DFR	X-ray	2.30	A	1-159	[»]
6DFR	X-ray	2.40	A	1-159	[»]
7DFR	X-ray	2.50	A	1-159	[»]

ProteinModelPortal

P0ABQ4.

SMR

P0ABQ4. Positions 1-159.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35824N.

IntAct

P0ABQ4. 10 interactions.

MINT

MINT-1239602.

STRING

511145.b0048.

2D gel databases

SWISS-2DPAGE

P0ABQ4.

Proteomic databases

PaxDb

P0ABQ4.

PRIDE

P0ABQ4.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73159; AAC73159; b0048.
BAB96616; BAB96616; BAB96616.

GeneID

12933205.
944790.

KEGG

ecj:Y75_p0048.
eco:b0048.

PATRIC

32115195. VBIEscCol129921_0049.

Organism-specific databases

EchoBASE

EB0322.

EcoGene

EG10326. folA.

Phylogenomic databases

eggNOG

COG0262.

HOGENOM

HOG000040233.

KO

K00287.

OMA

PTRFVVY.

ProtClustDB

PRK10769.

Enzyme and pathway databases

BioCyc

EcoCyc:DIHYDROFOLATEREDUCT-MONOMER.
ECOL316407:JW0047-MONOMER.
MetaCyc:DIHYDROFOLATEREDUCT-MONOMER.

SABIO-RK

P0ABQ4.

UniPathway

UPA00077; UER00158.

Gene expression databases

Genevestigator

P0ABQ4.

Family and domain databases

Gene3D

3.40.430.10. 1 hit.

InterPro

IPR012259. DHFR.
IPR024072. DHFR-like_dom.
IPR017925. DHFR_CS.
IPR001796. DHFR_dom.
[Graphical view]

Pfam

PF00186. DHFR_1. 1 hit.
[Graphical view]

PIRSF

PIRSF000194. DHFR. 1 hit.

PRINTS

PR00070. DHFR.

SUPFAM

SSF53597. SSF53597. 1 hit.

PROSITE

PS00075. DHFR_1. 1 hit.
PS51330. DHFR_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P0ABQ4.

ChEMBL

CHEMBL1809.

EvolutionaryTrace

P0ABQ4.

Entry information

Entry name

DYR_ECOLI

Accession

Primary (citable) accession number: P0ABQ4
Secondary accession number(s): P00379

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	May 1, 2013
This is version 81 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program