5X62

Crystal structure of a carnosine N-methyltransferase bound by AdoHcy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Substrate Recognition Mechanism of the Putative Yeast Carnosine N-methyltransferase

Liu, X.Wu, J.Sun, Y.Xie, W.

(2017) ACS Chem Biol 12: 2164-2171

  • DOI: 10.1021/acschembio.7b00328
  • Primary Citation of Related Structures:  
    5X62

  • PubMed Abstract: 
  • Anserine (β-alanyl-N(P i )-methyl-l-histidine) is a natural metabolite present in skeletal muscle and the central nervous system of vertebrates and plays important physiological roles in living organisms. The production of anserine is catalyzed by carnosine N-methyltransferases, which transfer a methyl group to carnosine (β-alanyl-l-histidine) ...

    Anserine (β-alanyl-N(P i )-methyl-l-histidine) is a natural metabolite present in skeletal muscle and the central nervous system of vertebrates and plays important physiological roles in living organisms. The production of anserine is catalyzed by carnosine N-methyltransferases, which transfer a methyl group to carnosine (β-alanyl-l-histidine). However, the structural basis of the substrate recognition for the enzymes is unknown. We present the crystal structure of the putative carnosine N-methyltransferase from yeast named YNL092W in complex with SAH, solved by the single-wavelength anomalous dispersion (SAD) method. The protein contains a typical Rossmann domain and a characteristic N-terminal helical domain. At the cofactor-binding site, SAH forms an extensive interaction network with the enzyme. The individual contribution of each residue to ligand affinity and enzyme activity was assessed by ITC and methyltransferase assays after mutagenesis of the key residues. Additionally, docking studies and activity assays were conducted in order to identify the binding site for carnosine, and a plausible complex model was proposed. Furthermore, we discovered that two disulfide bridges might be functionally important to the enzyme. By comparison to structure- and sequence-similar methyltransferases, we deduce that the enzyme most likely acts on a protein substrate. Our structural analyses shed light on the catalytic mechanism and substrate recognition by YNL092W.


    Organizational Affiliation

    Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University , 135 W. Xingang Rd., Guangzhou 510275, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carnosine N-methyltransferaseA, B406Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YNL092WN2227
EC: 2.1.1.22
UniProt
Find proteins for P53934 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53934 
Go to UniProtKB:  P53934
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.537α = 90
b = 72.902β = 90
c = 175.235γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-02-20 
  • Released Date: 2017-07-26 
  • Deposition Author(s): Xie, W., Liu, X.

Funding OrganizationLocationGrant Number
the Fundamental Research Funds for the Central UniversitiesChina16lgjc76
the Science and Technology Program of GuangzhouChina201504010025

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Database references