2YDX

Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Insight Into S-Adenosylmethionine Biosynthesis from the Crystal Structures of the Human Methionine Adenosyltransferase Catalytic and Regulatory Subunits.

Shafqat, N.Muniz, J.R.C.Pilka, E.S.Papagrigoriou, E.von Delft, F.Oppermann, U.Yue, W.W.

(2013) Biochem J 452: 27

  • DOI: https://doi.org/10.1042/BJ20121580
  • Primary Citation of Related Structures:  
    2YDX, 2YDY

  • PubMed Abstract: 

    MAT (methionine adenosyltransferase) utilizes L-methionine and ATP to form SAM (S-adenosylmethionine), the principal methyl donor in biological methylation. Mammals encode a liver-specific isoenzyme, MAT1A, that is genetically linked with an inborn metabolic disorder of hypermethioninaemia, as well as a ubiquitously expressed isoenzyme, MAT2A, whose enzymatic activity is regulated by an associated subunit MAT2B. To understand the molecular mechanism of MAT functions and interactions, we have crystallized the ligand-bound complexes of human MAT1A, MAT2A and MAT2B. The structures of MAT1A and MAT2A in binary complexes with their product SAM allow for a comparison with the Escherichia coli and rat structures. This facilitates the understanding of the different substrate or product conformations, mediated by the neighbouring gating loop, which can be accommodated by the compact active site during catalysis. The structure of MAT2B reveals an SDR (short-chain dehydrogenase/reductase) core with specificity for the NADP/H cofactor, and harbours the SDR catalytic triad (YxxxKS). Extended from the MAT2B core is a second domain with homology with an SDR sub-family that binds nucleotide-sugar substrates, although the equivalent region in MAT2B presents a more open and extended surface which may endow a different ligand/protein-binding capability. Together, the results of the present study provide a framework to assign structural features to the functional and catalytic properties of the human MAT proteins, and facilitate future studies to probe new catalytic and binding functions.


  • Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
A, B, C, D, E
315Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZL9 (Homo sapiens)
Explore Q9NZL9 
Go to UniProtKB:  Q9NZL9
PHAROS:  Q9NZL9
GTEx:  ENSG00000038274 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZL9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TXP
Query on TXP

Download Ideal Coordinates CCD File 
JA [auth E]1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE
C21 H32 N7 O17 P3
MGWIKFWDIJJFDG-ILTSWSAWSA-N
NAP
Query on NAP

Download Ideal Coordinates CCD File 
DA [auth D],
H [auth A],
P [auth B],
X [auth C]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
STL
Query on STL

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
F [auth A]
G [auth A]
HA [auth E]
BA [auth D],
CA [auth D],
F [auth A],
G [auth A],
HA [auth E],
IA [auth E],
N [auth B],
O [auth B],
V [auth C],
W [auth C]
RESVERATROL
C14 H12 O3
LUKBXSAWLPMMSZ-OWOJBTEDSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
EA [auth D]
FA [auth D]
GA [auth D]
I [auth A]
AA [auth C],
EA [auth D],
FA [auth D],
GA [auth D],
I [auth A],
J [auth A],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
MA [auth E],
NA [auth E],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.389α = 90
b = 163.389β = 90
c = 252.882γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references, Structure summary, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other