3LLD

Crystal structure of the mutant S127G of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/bi100443a
  • Primary Citation of Related Structures:  
    3LHT, 3LHU, 3LHV, 3LHW, 3LHY, 3LHZ, 3LI1, 3LLD, 3LLF, 3LTP, 3LTS, 3LTY, 3LV5, 3LV6, 3M1Z, 3M41, 3M43, 3M44, 3M47, 3M5X, 3M5Y, 3M5Z

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orotidine 5'-phosphate decarboxylase
A, B
228Methanothermobacter thermautotrophicus str. Delta HMutation(s): 2 
Gene Names: pyrFMTH_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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26232
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UP6
Query on UP6

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-AZA URIDINE 5'-MONOPHOSPHATE
C8 H12 N3 O9 P
LRVZOSYMNMNQFR-SHUUEZRQSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UP6 BindingDB:  3LLD Ki: 1.24e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.779α = 90
b = 63.638β = 115.19
c = 61.119γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
BALBESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description