3APY

Properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb3APY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-10-21 Released: 2011-09-14
Deposition Author(s): Yamada, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.306
R-Value Work: 0.204
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Properties and Crystal Structure of Methylenetetrahydrofolate Reductase from Thermus thermophilus HB8.

Igari, S., Ohtaki, A., Yamanaka, Y., Sato, Y., Yohda, M., Odaka, M., Noguchi, K., Yamada, K.

(2011) PLoS One 6: e23716-e23716

PubMed: 21858212 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0023716
Primary Citation of Related Structures:
3APT, 3APY

PubMed Abstract:
Methylenetetrahydrofolate reductase (MTHFR) is one of the enzymes involved in homocysteine metabolism. Despite considerable genetic and clinical attention, the reaction mechanism and regulation of this enzyme are not fully understood because of difficult production and poor stability. While recombinant enzymes from thermophilic organisms are often stable and easy to prepare, properties of thermostable MTHFRs have not yet been reported.

Organizational Affiliation

Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan.

Macromolecule Content

Total Structure Weight: 283.69 kDa
Atom Count: 19,755
Modelled Residue Count: 2,328
Deposited Residue Count: 2,480
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylenetetrahydrofolate reductase	A, B, C, D, E A, B, C, D, E, F, G, H	310	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA0327 EC: 1.5.1.20
UniProt
Find proteins for Q5SLG6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLG6 Go to UniProtKB: Q5SLG6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SLG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] SDF format, chain S [auth G] SDF format, chain U [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth G] MOL2 format, chain U [auth H]	I [auth A] K [auth B] L [auth C] M [auth D] O [auth E] I [auth A], K [auth B], L [auth C], M [auth D], O [auth E], Q [auth F], S [auth G], U [auth H]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain U [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain U [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain T [auth G] SDF format, chain V [auth H] MOL2 format, chain J [auth A] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain T [auth G] MOL2 format, chain V [auth H]	J [auth A] N [auth D] P [auth E] R [auth F] T [auth G] J [auth A], N [auth D], P [auth E], R [auth F], T [auth G], V [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain V [auth H] Interactions & Density Focus chain J [auth A] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain V [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.306
R-Value Work: 0.204
R-Value Observed: 0.209
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.588	α = 90
b = 90.93	β = 90
c = 125.152	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-09-14

Deposition Author(s):

Yamada, K.

Revision History (Full details and data files)

Version 1.0: 2011-09-14
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3APY

Properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8

Properties and Crystal Structure of Methylenetetrahydrofolate Reductase from Thermus thermophilus HB8.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)