1BM5

THE SOLUTION STRUCTURE OF A SITE-DIRECTED MUTANT (R111M) OF HUMAN CELLULAR RETIONIC ACID BINDING PROTEIN-TYPE II, NMR, 31 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 75 
  • Conformers Submitted: 31 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST TOTAL ENERGY 

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This is version 1.2 of the entry. See complete history

Literature

NMR study suggests a major role for Arg111 in maintaining the structure and dynamical properties of type II human cellular retinoic acid binding protein.

Wang, L.Yan, H.

(1998) Biochemistry 37: 13021-13032

  • DOI: 10.1021/bi981021x

  • PubMed Abstract: 
  • The solution structure of a site-directed mutant of type-II human cellular retinoic acid binding protein (CRABPII) with Arg111 replaced by methionine (R111M) has been determined by NMR spectroscopy. The sequential assignments of the 1H and 15N resona ...

    The solution structure of a site-directed mutant of type-II human cellular retinoic acid binding protein (CRABPII) with Arg111 replaced by methionine (R111M) has been determined by NMR spectroscopy. The sequential assignments of the 1H and 15N resonances of apo-R111M were established by multinuclear multidimensional NMR. The solution structure was calculated from 2302 distance restraints and 77 phi dihedral restraints derived from the NMR data. The root-mean-square deviation of the ensemble of 28 refined conformers that represent the structure from the mean coordinate set derived from them was 0.54 +/- 0.26 and 0.98 +/- 0.23 A for the backbone atoms and all heavy atoms, respectively. The solution structure of apo-R111M is similar to that of wild-type apo-CRABPII. However, there are significant conformational differences between the two proteins, localized mainly to three segments (Leu19-Ala36, Glu73-Cys81, and Leu99-Pro105) clustered around the ligand entrance more than 17 A away from the point mutation. In apo-R111M, all the three segments move toward the center of the ligand entrance so that the opening of the ligand-binding pocket in apo-R111M is much smaller than that in wild-type apo-CRABPII. Furthermore, the ligand-binding pocket of apo-R111M, especially the ligand entrance, is much less flexible than that of apo-CRABPII. Surprisingly, apo-R111M is more similar to holo-CRABPII than to apo-CRABPII in both structure and dynamical properties. The conformational and dynamical changes caused by the mutation are similar to those induced by binding of RA, although the magnitudes of the changes caused by the mutation are smaller than those induced by binding of RA. The results suggest that Arg111 plays a critical role in determining the structure and dynamical properties of CRABPII.


    Organizational Affiliation

    Department of Biochemistry, Michigan State University, East Lansing 48824, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELLULAR RETINOIC ACID BINDING PROTEIN-TYPE II
A
137Homo sapiensGene Names: CRABP2
Find proteins for P29373 (Homo sapiens)
Go to Gene View: CRABP2
Go to UniProtKB:  P29373
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 75 
  • Conformers Submitted: 31 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST TOTAL ENERGY 
  • Olderado: 1BM5 Olderado
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-07-28 
  • Released Date: 1999-01-13 
  • Deposition Author(s): Wang, H., Yan, H.

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance