1ZRR

Residual Dipolar Coupling Refinement of Acireductone Dioxygenase from Klebsiella


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 17 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A refined model for the structure of acireductone dioxygenase from Klebsiella ATCC 8724 incorporating residual dipolar couplings

Pochapsky, T.C.Pochapsky, S.S.Ju, T.Hoefler, C.Liang, J.

(2006) J.Biomol.NMR 34: 117-127

  • DOI: 10.1007/s10858-005-5735-8

  • PubMed Abstract: 
  • Acireductone dioxygenase (ARD) from Klebsiella ATCC 8724 is a metalloenzyme that is capable of catalyzing different reactions with the same substrates (acireductone and O2) depending upon the metal bound in the active site. A model for the solution s ...

    Acireductone dioxygenase (ARD) from Klebsiella ATCC 8724 is a metalloenzyme that is capable of catalyzing different reactions with the same substrates (acireductone and O2) depending upon the metal bound in the active site. A model for the solution structure of the paramagnetic Ni2+-containing ARD has been refined using residual dipolar couplings (RDCs) measured in two media. Additional dihedral restraints based on chemical shift (TALOS) were included in the refinement, and backbone structure in the vicinity of the active site was modeled from a crystallographic structure of the mouse homolog of ARD. The incorporation of residual dipolar couplings into the structural refinement alters the relative orientations of several structural features significantly, and improves local secondary structure determination. Comparisons between the solution structures obtained with and without RDCs are made, and structural similarities and differences between mouse and bacterial enzymes are described. Finally, the biological significance of these differences is considered.


    Related Citations: 
    • Mechanistic Studies of two Dioxygenases from the methionine salvage pathway of Klebsiella pneumoniae
      Dai, Y.,Pochapsky, T.C.,Abeles, R.H.
      (2001) Biochemistry 40: 6379
    • Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae
      Pochapsky, T.C.,Pochapsky, S.S.,Ju, T.,Mo, H.,Al-Mjeni, F.,Maroney, M.J.
      (2002) Nat.Struct.Mol.Biol. 9: 966


    Organizational Affiliation

    Department of Chemistry, Brandeis University, MS 015, 415 South Street, Waltham, MA 02454-9110, USA. pochapsk@brandeis.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E-2/E-2' protein
A
179Klebsiella oxytocaMutation(s): 0 
Gene Names: mtnD (masB)
Find proteins for Q9ZFE7 (Klebsiella oxytoca)
Go to UniProtKB:  Q9ZFE7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 17 
  • Olderado: 1ZRR Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance