Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 50.51 kDa 
• Atom Count: 3894 
• Modelled Residue Count: 438 
• Deposited Residue Count: 456 
• Unique protein chains: 1

3QF0

Crystal structure of the mutant T159V,Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP

• PDB DOI: 10.2210/pdb3QF0/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Methanothermobacter thermautotrophicus str. Delta H
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-01-20 Released: 2012-01-25 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.192 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.

Desai, B.J., Wood, B.M., Fedorov, A.A., Fedorov, E.V., Goryanova, B., Amyes, T.L., Richard, J.P., Almo, S.C., Gerlt, J.A.

(2012) Biochemistry 51: 8665-8678

• PubMed: 23030629 
• DOI: 10.1021/bi301188k
• Primary Citation of Related Structures:  
  3LI0, 3P5Y, 3P5Z, 3P60, 3P61, 3QEZ, 3QF0, 3QMR, 3QMS, 3QMT, 3RLU, 3RLV, 3SJ3, 3V1P, 4FX6, 4FX8, 4FXR, 4GC4


• PubMed Abstract: 
  

The binding of a ligand to orotidine 5'-monophosphate decarboxylase (OMPDC) is accompanied by a conformational change from an open, inactive conformation (E(o)) to a closed, active conformation (E(c)). As the substrate traverses the reaction coordinate to form the stabilized vinyl carbanion/carbene intermediate, interactions that destabilize the carboxylate group of the substrate and stabilize the intermediate (in the E(c)·S(‡) complex) are enforced. Focusing on the OMPDC from Methanothermobacter thermautotrophicus, we find the "remote" 5'-phosphate group of the substrate activates the enzyme 2.4 × 10(8)-fold; the activation is equivalently described by an intrinsic binding energy (IBE) of 11.4 kcal/mol. We studied residues in the activation that (1) directly contact the 5'-phosphate group, (2) participate in a hydrophobic cluster near the base of the active site loop that sequesters the bound substrate from the solvent, and (3) form hydrogen bonding interactions across the interface between the "mobile" and "fixed" half-barrel domains of the (β/α)(8)-barrel structure. Our data support a model in which the IBE provided by the 5'-phosphate group is used to allow interactions both near the N-terminus of the active site loop and across the domain interface that stabilize both the E(c)·S and E(c)·S(‡) complexes relative to the E(o)·S complex. The conclusion that the IBE of the 5'-phosphate group provides stabilization to both the E(c)·S and E(c)·S(‡) complexes, not just the E(c)·S(‡) complex, is central to understanding the structural origins of enzymatic catalysis as well as the requirements for the de novo design of enzymes that catalyze novel reactions.

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Organizational Affiliation: 

Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	228	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 2  Gene Names: pyrF, MTH_129 EC: 4.1.1.23
UniProt
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26232  Go to UniProtKB:  O26232

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMP	C [auth A], D [auth B]	6-HYDROXYURIDINE-5'-PHOSPHATE C9 H13 N2 O10 P UDOBICLZEKUKCV-YXZULKJRSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.192 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.93	α = 90
b = 63.675	β = 115.34
c = 61.432	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-20 
• Released Date: 2012-01-25 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references