3LTP

Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.

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

(2010) Biochemistry 49: 3514-3516

  • DOI: 10.1021/bi100443a
  • Primary Citation of Related Structures:  3LHT, 3LHU, 3LHV, 3LHW, 3LHY, 3LHZ, 3LI1, 3LLD, 3LLF, 3LTS, 3LTY, 3LV5, 3LV6, 3M41, 3M43, 3M44, 3M47, 3M5X, 3M5Y, 3M5Z, 3M1Z

  • PubMed Abstract: 
  • The structural factors responsible for the extraordinary rate enhancement ( approximately 10(17)) of the reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) have not been defined. Catalysis requires a conformational change that clo ...

    The structural factors responsible for the extraordinary rate enhancement ( approximately 10(17)) of the reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) have not been defined. Catalysis requires a conformational change that closes an active site loop and "clamps" the orotate base proximal to hydrogen-bonded networks that destabilize the substrate and stabilize the intermediate. In the OMPDC from Methanobacter thermoautotrophicus, a "remote" structurally conserved cluster of hydrophobic residues that includes Val 182 in the active site loop is assembled in the closed, catalytically active conformation. Substitution of these residues with Ala decreases k(cat)/K(m) with a minimal effect on k(cat), providing evidence that the cluster stabilizes the closed conformation. The intrinsic binding energies of the 5'-phosphate group of orotidine 5'-monophosphate for the mutant enzymes are similar to that for the wild type, supporting this conclusion.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orotidine 5'-phosphate decarboxylase
A, B
228Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)Gene Names: pyrF
EC: 4.1.1.23
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Go to UniProtKB:  O26232
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMP
Query on BMP

Download SDF File 
Download CCD File 
A, B
6-HYDROXYURIDINE-5'-PHOSPHATE
C9 H13 N2 O10 P
UDOBICLZEKUKCV-YXZULKJRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.772α = 90.00
b = 64.070β = 115.46
c = 61.639γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
ADSCdata collection
DENZOdata reduction
BALBESphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance