5VOO | pdb_00005voo

Methionine synthase folate-binding domain with methyltetrahydrofolate from Thermus thermophilus HB8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.230 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5VOO

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

The folate-binding module of Thermus thermophilus cobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'.

Yamada, K.Koutmos, M.

(2018) Acta Crystallogr D Struct Biol 74: 41-51

  • DOI: https://doi.org/10.1107/S2059798317018290
  • Primary Citation Related Structures: 
    5VON, 5VOO, 5VOP

  • PubMed Abstract: 

    Methyl transfer between methyltetrahydrofolate and corrinoid molecules is a key reaction in biology that is catalyzed by a number of enzymes in many prokaryotic and eukaryotic organisms. One classic example of such an enzyme is cobalamin-dependent methionine synthase (MS). MS is a large modular protein that utilizes an S N 2-type mechanism to catalyze the chemically challenging methyl transfer from the tertiary amine (N5) of methyltetrahydrofolate to homocysteine in order to form methionine. Despite over half a century of study, many questions remain about how folate-dependent methyltransferases, and MS in particular, function. Here, the structure of the folate-binding (Fol) domain of MS from Thermus thermophilus is reported in the presence and absence of methyltetrahydrofolate. It is found that the methyltetrahydrofolate-binding environment is similar to those of previously described methyltransferases, highlighting the conserved role of this domain in binding, and perhaps activating, the methyltetrahydrofolate substrate. These structural studies further reveal a new distinct and uncharacterized topology in the C-terminal region of MS Fol domains. Furthermore, it is found that in contrast to the canonical TIM-barrel β 8 α 8 fold found in all other folate-binding domains, MS Fol domains exhibit a unique β 8 α 7 fold. It is posited that these structural differences are important for MS function.


  • Organizational Affiliation
    • Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.

Macromolecule Content 

  • Total Structure Weight: 201.46 kDa 
  • Atom Count: 13,827 
  • Modeled Residue Count: 1,687 
  • Deposited Residue Count: 1,776 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5-methyltetrahydrofolate homocysteine S-methyltransferase
A, B, C, D, E
A, B, C, D, E, F
296Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0618
EC: 2.1.1.13
UniProt
Find proteins for Q5SKM5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKM5 
Go to UniProtKB:  Q5SKM5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKM5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2F

Query on C2F



Download:Ideal Coordinates CCD File
G [auth A]
M [auth B]
Q [auth C]
R [auth D]
U [auth E]
G [auth A],
M [auth B],
Q [auth C],
R [auth D],
U [auth E],
W [auth F]
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
C20 H25 N7 O6
ZNOVTXRBGFNYRX-STQMWFEESA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
T [auth D],
V [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
L [auth B],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth A],
P [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
N [auth B]
S [auth D]
H [auth A],
I [auth A],
J [auth A],
N [auth B],
S [auth D],
X [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.463α = 90
b = 188.463β = 90
c = 247.137γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States13SDG14560056

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description