4FIO

Crystal Structure of Methenyltetrahydromethanopterin Cyclohydrolase from Methanobrevibacter ruminantium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

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This is version 1.1 of the entry. See complete history. 


Literature

The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from Methanobrevibacter ruminantium.

Carbone, V., Schofield, L.R., Beattie, A.K., Sutherland-Smith, A.J., Ronimus, R.S.

(2013) Proteins 81: 2064-2070

  • DOI: 10.1002/prot.24372
  • Primary Citation of Related Structures:  
    4FIO

  • PubMed Abstract: 

    • Methenyltetrahydromethanopterin cyclohydrolase (Mch) is involved in the methanogenesis pathway of archaea as a C1 unit carrier where N(5) -formyl-tetrahydromethanopterin is converted to methenyl-tetrahydromethanopterin. Mch from Methanobrevibacter ruminantium was cloned, purified, crystallized and its crystal structure solved at 1 ...

    Methenyltetrahydromethanopterin cyclohydrolase (Mch) is involved in the methanogenesis pathway of archaea as a C1 unit carrier where N(5) -formyl-tetrahydromethanopterin is converted to methenyl-tetrahydromethanopterin. Mch from Methanobrevibacter ruminantium was cloned, purified, crystallized and its crystal structure solved at 1.37 Å resolution. A biologically active trimer, the enzyme is composed of two domains including an N-terminal domain of six α-helices encompassing a series of four β-sheets and a predominantly anti-parallel β-sheet at the C-terminus flanked on one side by α-helices. Sequence and structural alignments have helped identify residues involved in substrate binding and trimer formation.

    Organizational Affiliation: 

    AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methenyltetrahydromethanopterin cyclohydrolaseA, B, C354Methanobrevibacter ruminantium M1Mutation(s): 0 
Gene Names: mch, mru_1619
EC: 3.5.4.27
Find proteins for D3E4S5 (Methanobrevibacter ruminantium (strain ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1))
Explore D3E4S5 
Go to UniProtKB:  D3E4S5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EEE
Query on EEE
Download Ideal Coordinates CCD File 
 D [auth A], F [auth B]ETHYL ACETATE
C4 H8 O2
XEKOWRVHYACXOJ-UHFFFAOYSA-N		 Ligand Interaction
IPA
Query on IPA
Download Ideal Coordinates CCD File 
 E [auth A], G [auth B], H [auth B]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.37α = 120.06
b = 74.855β = 100.01
c = 74.816γ = 98.28
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references