Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 185.6 kDa 
• Atom Count: 13,178 
• Modelled Residue Count: 1,560 
• Deposited Residue Count: 1,575 
• Unique protein chains: 1

 2YDX

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

• PDB DOI: 10.2210/pdb2YDX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-25 Released: 2011-04-27 
• Deposition Author(s): Muniz, J.R.C., Shafqat, N., Pike, A.C.W., Yue, W.W., Vollmar, M., Papagriogriou, V., Roos, A., Gileadi, O., von Delft, F., Kavanagh, K.L., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Oppermann, U.

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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 

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

• PubMed: 23425511 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA	A, B, C, D, E	315	Homo sapiens	Mutation(s): 0  Gene Names: MAT2B, TGR, MSTP045, Nbla02999, UNQ2435/PRO4995
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZL9 (Homo sapiens) Explore Q9NZL9  Go to UniProtKB:  Q9NZL9
PHAROS:  Q9NZL9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TXP	JA [auth E]	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE C21 H32 N7 O17 P3 MGWIKFWDIJJFDG-ILTSWSAWSA-N
NAP	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	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	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	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 = 163.389	α = 90
b = 163.389	β = 90
c = 252.882	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Muniz, J.R.C., Shafqat, N., Pike, A.C.W., Yue, W.W., Vollmar, M., Papagriogriou, V., Roos, A., Gileadi, O., von Delft, F., Kavanagh, K.L., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Oppermann, U.

Revision History  

• 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