2AVF

Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of C-terminal desundecapeptide nitrite reductase from Achromobacter cycloclastes

Li, H.T., Chang, T., Chang, W.C., Chen, C.J., Liu, M.Y., Gui, L.L., Zhang, J.P., An, X.M., Chang, W.R.

(2005) Biochem Biophys Res Commun 338: 1935-1942

  • DOI: 10.1016/j.bbrc.2005.09.199
  • Primary Citation of Related Structures:  
    2AVF

  • PubMed Abstract: 

    • Monoclinic crystal structure of C-terminal desundecapeptide nitrite reductase (NiRc-11) from Achromobacter cycloclastes was determined at 2.6A. NiRc-11 exists as a loose trimer in the crystal. Deletion of 11 residues eliminates all intersubunit hydro ...

    Monoclinic crystal structure of C-terminal desundecapeptide nitrite reductase (NiRc-11) from Achromobacter cycloclastes was determined at 2.6A. NiRc-11 exists as a loose trimer in the crystal. Deletion of 11 residues eliminates all intersubunit hydrogen bonds mediated by the C-terminal tail. The rigid irregular coil 105-112, which constitutes part of the sidewall of the active site pocket, undergoes conformational changes and becomes highly flexible in NiRc-11. Correspondingly, the linker segments between the two copper sites 95-100 and 135-136 are partly relaxed in conformation, which leads to disrupted active site microenvironments responsible for the activity loss and spectral change of NiRc-11. Comparison with the native structure revealed a bulky residue Met331 fastened by hydrogen bonding, which may play a direct role in keeping the right copper site geometry by protruding its side chain against the irregular coil 105-112. Sequence alignment showed that the bulky residue is conserved at position 331, indicating an equal importance of C-terminal segment in other copper-containing nitrite reductases.

    Organizational Affiliation: 

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15th Datun Road, Chaoyang District, Beijing 100101, China.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-containing nitrite reductaseA, B, C, D, E, F329Achromobacter cycloclastesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
Find proteins for P25006 (Achromobacter cycloclastes)
Explore P25006 
Go to UniProtKB:  P25006
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.783α = 90
b = 111.072β = 101.67
c = 122.884γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance