4GVQ

X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase in complex with tetrahydromethanpterin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and catalytic mechanism of N(5),N(10)-methenyl-tetrahydromethanopterin cyclohydrolase.

Upadhyay, V.Demmer, U.Warkentin, E.Moll, J.Shima, S.Ermler, U.

(2012) Biochemistry 51: 8435-8443

  • DOI: 10.1021/bi300777k
  • Primary Citation of Related Structures:  
    4GVS, 4GVQ, 4GVR

  • PubMed Abstract: 
  • Methenyltetrahydromethanopterin (methenyl-H(4)MPT(+)) cyclohydrolase (Mch) catalyzes the interconversion of methenyl-H(4)MPT(+) and formyl-H(4)MPT in the one-carbon energy metabolism of methanogenic, methanotrophic, and sulfate-reducing archaea and of methylotrophic bacteria ...

    Methenyltetrahydromethanopterin (methenyl-H(4)MPT(+)) cyclohydrolase (Mch) catalyzes the interconversion of methenyl-H(4)MPT(+) and formyl-H(4)MPT in the one-carbon energy metabolism of methanogenic, methanotrophic, and sulfate-reducing archaea and of methylotrophic bacteria. To understand the catalytic mechanism of this reaction, we kinetically characterized site-specific variants of Mch from Archaeoglobus fulgidus (aMch) and determined the X-ray structures of the substrate-free aMch(E186Q), the aMch:H(4)MPT complex, and the aMch(E186Q):formyl-H(4)MPT complex. (Formyl-)H(4)MPT is embedded inside a largely preformed, interdomain pocket of the homotrimeric enzyme with the pterin and benzyl rings being oriented nearly perpendicular to each other. The active site is primarily built up by the segment 93:95, Arg183 and Glu186 that either interact with the catalytic water attacking methenyl-H(4)MPT(+) or with the formyl oxygen of formyl-H(4)MPT. The catalytic function of the strictly conserved Arg183 and Glu186 was substantiated by the low enzymatic activities of the E186A, E186D, E186N, E186Q, R183A, R183Q, R183E, R183K, and R183E-E186Q variants. Glu186 most likely acts as a general base. Arg183 decisively influences the pK(a) value of Glu186 and the proposed catalytic water mainly by its positive charge. In addition, Glu186 appears to be also responsible for product specificity by donating a proton to the directly neighbored N(10) tertiary amine of H(4)MPT. Thus, N(10) becomes a better leaving group than N(5) which implies the generation of N(5)-formyl-H(4)MPT. For comparison, methenyltetrahydrofolate (H(4)F) cyclohydrolase produces N(10)-formyl-H(4)F in an analogous reaction. An enzymatic mechanism of Mch is postulated and compared with that of other cyclohydrolases.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methenyltetrahydromethanopterin cyclohydrolase ABC316Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: AF_1935mch
EC: 3.5.4.27
Find proteins for O28344 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O28344 
Go to UniProtKB:  O28344
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N4M
Query on N4M

Download Ideal Coordinates CCD File 
A, B
1-[4-({(1R)-1-[(6S,7S)-2-amino-7-methyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]ethyl}amino)phenyl]-1-deoxy-5-O-{5-O-[(R)-{[(1R)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-xylitol
C30 H45 N6 O16 P
SCBIBGUJSMHIAI-FQVOATFZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.597α = 90
b = 94.204β = 90
c = 114.856γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references