4FIO | pdb_00004fio

Crystal Structure of Methenyltetrahydromethanopterin Cyclohydrolase from Methanobrevibacter ruminantium

• PDB DOI: https://doi.org/10.2210/pdb4FIO/pdb

• Classification: HYDROLASE
• Organism(s): Methanobrevibacter ruminantium M1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-06-10 Released: 2013-07-24 
• Deposition Author(s): Carbone, V., Schofield, L.R., Beattie, A.K., Sutherland-Smith, A.J., Ronimus, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.175 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.124 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

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

• PubMed: 23873651 
• DOI: https://doi.org/10.1002/prot.24372
• Primary Citation 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 1.37 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 113.58 kDa 
• Atom Count: 8,472 
• Modeled Residue Count: 960 
• Deposited Residue Count: 1,062 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methenyltetrahydromethanopterin cyclohydrolase	A, B, C	354	Methanobrevibacter ruminantium M1	Mutation(s): 0  Gene Names: mch, mru_1619 EC: 3.5.4.27
UniProt
Find proteins for D3E4S5 (Methanobrevibacter ruminantium (strain ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1)) Explore D3E4S5  Go to UniProtKB:  D3E4S5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EEE	D [auth A], F [auth B]	ETHYL ACETATE C4 H8 O2 XEKOWRVHYACXOJ-UHFFFAOYSA-N
IPA	E [auth A], G [auth B], H [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.175 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.124 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.37	α = 120.06
b = 74.855	β = 100.01
c = 74.816	γ = 98.28

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Carbone, V., Schofield, L.R., Beattie, A.K., Sutherland-Smith, A.J., Ronimus, R.S.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2019-07-03
  Changes: Data collection, Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description