6RK7 | pdb_00006rk7

Inter-dimeric interface controls function and stability of S-methionine adenosyltransferase from U. urealiticum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.194 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase.

Kleiner, D.Shmulevich, F.Zarivach, R.Shahar, A.Sharon, M.Ben-Nissan, G.Bershtein, S.

(2019) J Mol Biology 431: 4796-4816

  • DOI: https://doi.org/10.1016/j.jmb.2019.09.003
  • Primary Citation Related Structures: 
    6RJS, 6RK5, 6RK7, 6RKA, 6RKC

  • PubMed Abstract: 

    Methionine S-adenosyltransferases (MATs) are predominantly homotetramers, comprised of dimers of dimers. The larger, highly conserved intradimeric interface harbors two active sites, making the dimer the obligatory functional unit. However, functionality of the smaller, more diverged, and recently evolved interdimeric interface is largely unknown. Here, we show that the interdimeric interface of Ureaplasmaurealiticum MAT has evolved to control the catalytic activity and structural integrity of the homotetramer in response to product accumulation. When all four active sites are occupied with the product, S-adenosylmethionine (SAM), binding of four additional SAM molecules to the interdimeric interface prompts a ∼45° shift in the dimer orientation and a concomitant ∼60% increase in the interface area. This rearrangement inhibits the enzymatic activity by locking the flexible active site loops in a closed state and renders the tetramer resistant to proteolytic degradation. Our findings suggest that the interdimeric interface of MATs is subject to rapid evolutionary changes that tailor the molecular properties of the entire homotetramer to the specific needs of the organism.


  • Organizational Affiliation
    • Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel.

Macromolecule Content 

  • Total Structure Weight: 262.28 kDa 
  • Atom Count: 19,574 
  • Modeled Residue Count: 2,245 
  • Deposited Residue Count: 2,292 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methionine adenosyltransferase382Ureaplasma urealyticum serovar 7 str. ATCC 27819Mutation(s): 0 
Gene Names: metKUUR7_0462
EC: 2.5.1.6

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM

Query on SAM



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
J [auth B]
K [auth B]
M [auth E]
G [auth A],
H [auth A],
J [auth B],
K [auth B],
M [auth E],
N [auth E],
P [auth F],
Q [auth F],
S [auth G],
T [auth G],
V [auth H],
W [auth H]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A]
L [auth B]
O [auth E]
R [auth F]
U [auth G]
I [auth A],
L [auth B],
O [auth E],
R [auth F],
U [auth G],
X [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.194 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.999α = 90
b = 106.139β = 96.86
c = 234.377γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael1630/15

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description