1CTU

TRANSITION-STATE SELECTIVITY FOR A SINGLE OH GROUP DURING CATALYSIS BY CYTIDINE DEAMINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase.

Xiang, S.Short, S.A.Wolfenden, R.Carter Jr., C.W.

(1995) Biochemistry 34: 4516-4523

  • Primary Citation of Related Structures:  1CTT

  • PubMed Abstract: 
  • Cytidine deaminase binds transition-state analog inhibitors approximately 10(7) times more tightly than corresponding 3,4-dihydro analogs containing a proton in place of the 4-hydroxyl group. X-ray crystal structures of complexes with the two matched ...

    Cytidine deaminase binds transition-state analog inhibitors approximately 10(7) times more tightly than corresponding 3,4-dihydro analogs containing a proton in place of the 4-hydroxyl group. X-ray crystal structures of complexes with the two matched inhibitors differ only near a "trapped" water molecule in the complex with the 3,4-dihydro analog, where contacts are substantially less favorable than those with the hydroxyl group of the transition-state analog. The hydrogen bond between the hydroxyl group and the Glu 104 carboxylate shortens in that complex, and may become a "low-barrier" hydrogen bond, since at the same time the bond between zinc and the Cys 132 thiolate ligand lengthens. These differences must therefore account for most of the differential binding affinity related to catalysis. Moreover, the trapped water molecule retains some of the binding energy stabilizing the hydroxyl group in the transition-state analog complex. To this extent, the ratio of binding affinities for the two compounds is smaller than the true contribution of the hydroxyl group, a conclusion with significant bearing on interpreting difference free energies derived from substituent effects arising from chemical modification and/or mutagenesis.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill 27599-7260, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTIDINE DEAMINASE
A
294Escherichia coli (strain K12)Gene Names: cdd
EC: 3.5.4.5
Find proteins for P0ABF6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABF6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ZEB
Query on ZEB

Download SDF File 
Download CCD File 
A
4-HYDROXY-3,4-DIHYDRO-ZEBULARINE
C9 H14 N2 O6
LUOTYVSEHPPZEM-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZEBKi: 0.0012 nM BINDINGMOAD
ZEBKi: 0.0012 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.190 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 120.300α = 90.00
b = 120.300β = 90.00
c = 78.400γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
R-AXISdata reduction
X-PLORrefinement
X-PLORphasing
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-05-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance