PDBsum entry 1b5t

Oxidoreductase

PDB id: 1b5t

Contents

Protein chains

275 a.a. *

Ligands

FAD ×3

Metals

_HG ×3

Waters ×184

* Residue conservation analysis

PDB id:

1b5t

Name:

Oxidoreductase

Title:

Escherichia coli methylenetetrahydrofolate reductase

Structure:

Protein (methylenetetrahydrofolate reductase). Chain: a, b, c. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: metf. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.212 R-free: 0.263

Authors:

B.D.Guenther,C.A.Sheppard,P.Tran,R.Rozen,R.G.Matthews,M.L.Ludwig

Key ref:

B.D.Guenther et al. (1999). The structure and properties of methylenetetrahydrofolate reductase from Escherichia coli suggest how folate ameliorates human hyperhomocysteinemia. Nat Struct Biol, 6, 359-365. PubMed id: 10201405 DOI: 10.1038/7594

Date:

07-Jan-99 Release date: 20-Jan-99

Protein chains

P0AEZ1  (METF_ECOLI) -  5,10-methylenetetrahydrofolate reductase from Escherichia coli (strain K12)

Seq: 296 a.a.

Struc: 275 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.5.1.54 - methylenetetrahydrofolate reductase (NADH).
• Reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + NAD⁺ = (6R)-5,10-methylene- 5,6,7,8-tetrahydrofolate + NADH + H⁺

(6S)-5-methyl-5,6,7,8-tetrahydrofolate + NAD(+) (Bound ligand (Het Group name = FAD) matches with 76.36% similarity) = (6R)-5,10-methylene- 5,6,7,8-tetrahydrofolate + NADH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/7594

Nat Struct Biol 6:359-365 (1999)

PubMed id: 10201405

The structure and properties of methylenetetrahydrofolate reductase from Escherichia coli suggest how folate ameliorates human hyperhomocysteinemia.

B.D.Guenther, C.A.Sheppard, P.Tran, R.Rozen, R.G.Matthews, M.L.Ludwig.

ABSTRACT

Elevated plasma homocysteine levels are associated with increased risk for cardiovascular disease and neural tube defects in humans. Folate treatment decreases homocysteine levels and dramatically reduces the incidence of neural tube defects. The flavoprotein methylenetetrahydrofolate reductase (MTHFR) is a likely target for these actions of folate. The most common genetic cause of mildly elevated plasma homocysteine in humans is the MTHFR polymorphism A222V (base change C677-->T). The X-ray analysis of E. coli MTHFR, reported here, provides a model for the catalytic domain that is shared by all MTHFRs. This domain is a beta8alpha8 barrel that binds FAD in a novel fashion. Ala 177, corresponding to Ala 222 in human MTHFR, is near the bottom of the barrel and distant from the FAD. The mutation A177V does not affect Km or k(cat) but instead increases the propensity for bacterial MTHFR to lose its essential flavin cofactor. Folate derivatives protect wild-type and mutant E. coli enzymes against flavin loss, and protect human MTHFR and the A222V mutant against thermal inactivation, suggesting a mechanism by which folate treatment reduces homocysteine levels.

Selected figure(s)

Figure 2.
Figure 2. The structure of E. coli MTHFR. a, A view along the axis of the [8] [8] barrel looking toward the C-terminal ends of the −strands^37. FAD is drawn in ball-and-stick mode. Helix 5, which precedes the site corresponding to the human A arrow V polymorphism, is colored red in this and succeeding figures. b, A view perpendicular to the barrel axis and toward the si face of the flavin ring, showing the truncation of strand 8 and helix 8 and the resulting groove in which methylenetetrahydrofolate is expected to bind. Ala 177, the site of the Ala arrow Val mutation, is drawn with gray dot surfaces, and is at the rear of the barrel. c, A stereo drawing of the chain fold from approximately the same perspective as in ( a).

Figure 6.
Figure 6. a, The location and environment of the Ala 177 that corresponds to the site of the A arrow V polymorphism in human MTHFR. The view is approximately perpendicular to the barrel axis and oriented to show helix 5 and its neighboring barrel strands. Black dot surfaces trace the helix backbone from 171 to 176; red surfaces represent the volume of alanine at position 177, and green surfaces a valine substituted at position 177 which clearly overlaps the helix backbone. The side chains of Lys 172, Asn 168, and Asp 165 that interact with FAD are drawn in ball-and-stick mode with carbons in cyan. b, The tetramer of E. coli MTHFR, viewed down the local two-fold axis. The asymmetric unit of the monoclinic cell contains the three chains A, B, and C; the fourth chain of the tetramer (A') is related to A by a crystallographic two-fold axis. The C and B subunits can be superimposed on chains A and A' by a local dyad (perpendicular to the page) that is inclined by ~53° to the crystallographic dyad along axis y. This local dyad is the only symmetry operator that relates the chains of the tetramer to one another. Interfaces A−A' and B−C are formed by symmetric interactions between helices 7c, 7b, and 8. In contrast, the A and B (or C and A') chains are not related by a simple rotation of 360/n^O; the B chain is superimposed on the A chain by a rotation of 108° and a translation of ~7 Å. Helix 5, which may be critical in mediating the effects of mutation at position 177, is drawn in red, and Ala 177 is white and surrounded by dot surfaces. The figure was prepared using the program RIBBONS^37.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 359-365) copyright 1999.

Figures were selected by an automated process.