1T23

NMR Solution Structure of the Archaebacterial Chromosomal Protein MC1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

NMR Solution Structure of the Archaebacterial Chromosomal Protein MC1 Reveals a New Protein Fold

Paquet, F.Culard, F.Barbault, F.Maurizot, J.C.Lancelot, G.

(2004) Biochemistry 43: 14971-14978

  • DOI: https://doi.org/10.1021/bi048382z
  • Primary Citation of Related Structures:  
    1T23

  • PubMed Abstract: 

    The three-dimensional structure of methanogen chromosomal protein 1 (MC1), a chromosomal protein extracted from the archaebacterium Methanosarcina sp. CHTI55, has been solved using (1)H NMR spectroscopy. The small basic protein MC1 contains 93 amino acids (24 basic residues against 12 acidic residues). The main elements of secondary structures are an alpha helix and five beta strands, arranged as two antiparallel beta sheets (a double one and a triple one) packed in an orthogonal manner forming a barrel. The protein displays a largely hydrophilic surface and a very compact hydrophobic core made up by side chains at the interface of the two beta sheets and the helix side facing the interior of the protein. The MC1 solution structure shows a globular protein with overall dimensions in the range of 34-40 A, which potentially corresponds to a DNA-binding site of 10-12 base pairs. The presumed DNA-binding site is located on the sequence comprising residues K62-P82, which is formed by a part of strands II2 and II3 belonging to the triple-stranded antiparallel beta sheet and a loop flanked by prolines P68 and P76. The tryptophan W74 that is expected to play a key role in the DNA-binding according to photocross-linking experiments was found completely exposed to the solvent, in a good position to interact with DNA. The overall fold of MC1, characterized by its linking beta-beta-alpha-beta-beta-loop-beta, is different from other known DNA-binding proteins. Its structure suggests a different DNA-binding mode than those of the histone-like proteins HU or HMGB. Thus, MC1 may be classified as a member of a new family.


  • Organizational Affiliation

    Centre de Biophysique Moléculaire, CNRS, Rue Charles Sadron, 45071 Orléans Cedex 2, France. paquet@cnrs-orleans.fr


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosomal protein MC193Methanosarcina thermophilaMutation(s): 0 
UniProt
Find proteins for P12770 (Methanosarcina thermophila)
Explore P12770 
Go to UniProtKB:  P12770
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12770
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection