3DHZ

Apo (iron free) structure of C. ammoniagenes R2 protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


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

Literature

Structural and mutational studies of the carboxylate cluster in Iron-free Ribonucleotide Reductase R2.

Andersson, M.E., Hogbom, M., Rinaldo-Matthis, A., Blodig, W., Liang, Y., Persson, B.O., Sjoberg, B.M., Su, X.D., Nordlund, P.

(2004) Biochemistry 43: 7966-7972

  • DOI: 10.1021/bi036088l

  • PubMed Abstract: 

    • The R2 protein of ribonucleotide reductase features a di-iron site deeply buried in the protein interior. The apo form of the R2 protein has an unusual clustering of carboxylate side chains at the empty metal-binding site. In a previous study, it was ...

    The R2 protein of ribonucleotide reductase features a di-iron site deeply buried in the protein interior. The apo form of the R2 protein has an unusual clustering of carboxylate side chains at the empty metal-binding site. In a previous study, it was found that the loss of the four positive charge equivalents of the diferrous site in the apo protein appeared to be compensated for by the protonation of two histidine and two carboxylate side chains. We have studied the consequences of removing and introducing charged residues on the local hydrogen-bonding pattern in the region of the carboxylate cluster of Corynebacterium ammoniagenes and Escherichia coli protein R2 using site-directed mutagenesis and X-ray crystallography. The structures of the metal-free forms of wild-type C. ammoniagenes R2 and the mutant E. coli proteins D84N, S114D, E115A, H118A, and E238A have been determined and their hydrogen bonding and protonation states have been structurally assigned as far as possible. Significant alterations to the hydrogen-bonding patterns, protonation states, and hydration is observed for all mutant E. coli apo proteins as compared to wild-type apo R2. Further structural variations are revealed by the wild-type apo C. ammoniagenes R2 structure. The protonation and hydration effects seen in the carboxylate cluster appear to be due to two major factors: conservation of the overall charge of the site and the requirement of electrostatic shielding of clustered carboxylate residues. Very short hydrogen-bonding distances between some protonated carboxylate pairs are indicative of low-barrier hydrogen bonding.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonucleotide reductase subunit R2F
A, B
329Corynebacterium ammoniagenesMutation(s): 0 
Gene Names: nrdF
EC: 1.17.4.1
Find proteins for O69274 (Corynebacterium ammoniagenes)
Go to UniProtKB:  O69274
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2
Download SDF File 
Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.908α = 90.00
b = 86.537β = 105.48
c = 70.610γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-03-07
    Type: Data collection