1A56

PRIMARY SEQUENCE AND SOLUTION CONFORMATION OF FERRICYTOCHROME C-552 FROM NITROSOMONAS EUROPAEA, NMR, MEAN STRUCTURE REFINED WITH EXPLICIT HYDROGEN BOND CONSTRAINTS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: MINIMUM ENERGY 

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This is version 1.2 of the entry. See complete history

Literature

Primary sequence and solution conformation of ferrocytochrome c-552 from Nitrosomonas europaea.

Timkovich, R.Bergmann, D.Arciero, D.M.Hooper, A.B.

(1998) Biophys.J. 75: 1964-1972

  • DOI: 10.1016/S0006-3495(98)77637-4
  • Primary Citation of Related Structures:  1A8C

  • PubMed Abstract: 
  • Cytochrome c-552 from Nitrosomonas europaea is a 9.1-kDa monoheme protein that is a member of the bacterial cytochrome c-551 family. The gene encoding for c-552 has been cloned and sequenced and the primary sequence of the product deduced. Proton res ...

    Cytochrome c-552 from Nitrosomonas europaea is a 9.1-kDa monoheme protein that is a member of the bacterial cytochrome c-551 family. The gene encoding for c-552 has been cloned and sequenced and the primary sequence of the product deduced. Proton resonance assignments were made for all main-chain and most side-chain protons in the diamagnetic, reduced form by two-dimensional NMR techniques. Distance constraints (1056) were determined from nuclear Overhauser enhancements, and torsion angle constraints (88) were determined from scalar coupling estimates. Solution conformations for the protein were computed by the hybrid distance geometry-simulated annealing approach. For 20 computed structures, the root mean squared deviation from the average position of equivalent atoms was 0.84 A (sigma = 0.12) for backbone atoms over all residues. Analysis by residue revealed there were three regions clearly less well defined than the rest of the protein: the first two residues at the N-terminus, the last two at the C-terminus, and a loop region from residues 34 to 40. Omitting these regions from the comparison, the root mean squared deviation was 0.61 A (sigma = 0.13) for backbone atoms, 0.86 A (sigma = 0.12) for all associated heavy atoms, and 0. 43 A (sigma = 0.17) for the heme group. The global folding of the protein is consistent with others in the c-551 family. A deletion at the N-terminus relative to other family members had no impact on the global folding, whereas an insertion at residue 65 did affect the way the polypeptide packs against the methionine-ligated side of the heme. The effects of specific substitutions will be discussed. The structure of c-552 serves to delineate essential features of the c-551 family.


    Organizational Affiliation

    Department of Chemistry, University of Alabama, Tuscaloosa, Alabama 35487-0336, USA. rtimkovi@ualvm.ua.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERRICYTOCHROME C-552
A
81Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298)Gene Names: cyt (cyt_c552)
Find proteins for P95339 (Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298))
Go to UniProtKB:  P95339
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download SDF File 
Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: MINIMUM ENERGY 
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance