2JNV | pdb_00002jnv

Solution structure of C-terminal domain of NifU-like protein from Oryza sativa


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report

Validation slider image for 2JNV

This is version 1.3 of the entry. See complete history

Literature

The cooperative role of OsCnfU-1A domain I and domain II in the iron sulphur cluster transfer process as revealed by NMR

Saio, T.Kumeta, H.Ogura, K.Yokochi, M.Asayama, M.Katoh, S.Katoh, E.Teshima, K.Inagaki, F.

(2007) J Biochem 142: 113-121

  • DOI: https://doi.org/10.1093/jb/mvm120
  • Primary Citation Related Structures: 
    2JNV

  • PubMed Abstract: 

    OsCnfU-1A is a chloroplast-type Nfu-like protein that consists of tandem repeats sharing high sequence homology. Domain I of this protein, but not domain II, has a C-X-X-C motif that is thought to assemble an iron-sulphur cluster. Herein we report the solution structure of OsCnfU-1A domain I (73-153). Although OsCnfU-1A domain I is structurally similar to OsCnfU-1A domain II (154-226), the electrostatic surface potential of the 2 domains differs. Domain I has an acidic surface, whereas that of domain II is predominantly basic. Chemical shift perturbation studies on OsCnfU-1A domain I and domain II with ferredoxin revealed negligible chemical shift changes in domain I, whereas much larger chemical shift changes were observed in domain II. The residues with larger chemical shift changes were located on the basic surface of domain II. Considering that ferredoxin is predominantly negatively charged, we propose the following hypothesis: First, an iron-sulphur cluster is assembled on domain I. Next, domain II interacts with the ferredoxin, thus tethering domain I close to the ferredoxin. Finally, domain I transfers the iron-sulphur cluster to the ferredoxin. Thus, domain II facilitates the efficient transfer of the iron-sulphur cluster from domain I to the ferredoxin.


  • Organizational Affiliation
    • Laboratory of Structural Biology, Graduate School of Pharmaceutical Science, Hokkaido University, Sapporo, Hokkaido, Japan.

Macromolecule Content 

  • Total Structure Weight: 9.82 kDa 
  • Atom Count: 609 
  • Modeled Residue Count: 83 
  • Deposited Residue Count: 91 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NifU-like protein 1, chloroplast91Oryza sativaMutation(s): 0 
Gene Names: NIFU1
UniProt
Find proteins for Q84LK7 (Oryza sativa subsp. japonica)
Explore Q84LK7 
Go to UniProtKB:  Q84LK7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84LK7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-09
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-12-20
    Changes: Data collection, Other