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PDBsum entry 2r2f
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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2r2f

 

 

 

 

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Contents
Protein chains
286 a.a. *
Ligands
FEO ×2
Waters ×415
* Residue conservation analysis
PDB id:
2r2f
Name: Oxidoreductase
Title: Ribonucleotide reductase r2f protein from salmonella typhimurium (oxidized)
Structure: Protein (ribonucleoside-diphosphate reductase small chain). Chain: a, b. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.25Å     R-factor:   0.228     R-free:   0.268
Authors: H.Eklund,M.Eriksson
Key ref:
M.Eriksson et al. (1998). Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its oxidized and reduced forms. Biochemistry, 37, 13359-13369. PubMed id: 9748343 DOI: 10.1021/bi981380s
Date:
24-Aug-98     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P17424  (RIR4_SALTY) -  Ribonucleoside-diphosphate reductase 2 subunit beta from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Seq:
Struc: 		319 a.a.
286 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.17.4.1  - ribonucleoside-diphosphate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: a 2'-deoxyribonucleoside 5'-diphosphate + [thioredoxin]-disulfide + H2O = a ribonucleoside 5'-diphosphate + [thioredoxin]-dithiol
2'-deoxyribonucleoside diphosphate
 + thioredoxin disulfide
 + H(2)O
 = ribonucleoside diphosphate
 + thioredoxin
      Cofactor: Fe(3+) or adenosylcob(III)alamin or Mn(2+)
Fe(3+)
 or adenosylcob(III)alamin
 or Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/bi981380s Biochemistry 37:13359-13369 (1998)
PubMed id: 9748343  
 
 
Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its oxidized and reduced forms.
M.Eriksson, A.Jordan, H.Eklund.
 
  ABSTRACT  
 
The first class Ib ribonucleotide reductase R2 structure, from Salmonella typhimurium, has been determined at 2.0 A resolution. The overall structure is similar to the Escherichia coli class Ia enzyme despite only 23% sequence identity. The most spectacular difference is the absence of the pleated sheet and adjacent parts present in the E. coli R2 structure; the heart-shaped structure loses its tip. From sequence comparisons, it appears that this feature is shared with all other class Ib enzymes and, in this respect, is more like the mammalian class Ia enzymes. Both the oxidized and reduced iron forms have been investigated. In the ferric iron center, both iron ions are octahedrally coordinated and bridged by one carboxylate and one oxide ion. The ferrous form has lost the bridging oxide ion but is bridged by two carboxylates. Accompanying the change in redox state, helix E changes its conformation from one covering the metal center in the oxidized form to a more open reduced form. A narrow channel is opened which may permit easier access of oxygen to the ferrous iron site and to efficiently generate the tyrosyl radical.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20688982 A.K.Boal, J.A.Cotruvo, J.Stubbe, and A.C.Rosenzweig (2010).
Structural basis for activation of class Ib ribonucleotide reductase.
  Science, 329, 1526-1530.
PDB codes: 3n37 3n38 3n39 3n3a 3n3b
20831589 R.Johansson, E.Torrents, D.Lundin, J.Sprenger, M.Sahlin, B.M.Sjöberg, and D.T.Logan (2010).
High-resolution crystal structures of the flavoprotein NrdI in oxidized and reduced states--an unusual flavodoxin. Structural biology.
  FEBS J, 277, 4265-4277.
PDB codes: 2xod 2xoe
19639135 D.A.Svistunenko, and G.A.Jones (2009).
Tyrosyl radicals in proteins: a comparison of empirical and density functional calculated EPR parameters.
  Phys Chem Chem Phys, 11, 6600-6613.  
18799738 J.A.Cotruvo, and J.Stubbe (2008).
NrdI, a flavodoxin involved in maintenance of the diferric-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductase.
  Proc Natl Acad Sci U S A, 105, 14383-14388.  
19061340 W.Jiang, D.Yun, L.Saleh, J.M.Bollinger, and C.Krebs (2008).
Formation and function of the Manganese(IV)/Iron(III) cofactor in Chlamydia trachomatis ribonucleotide reductase.
  Biochemistry, 47, 13736-13744.  
16854982 M.Galander, M.Uppsten, U.Uhlin, and F.Lendzian (2006).
Orientation of the tyrosyl radical in Salmonella typhimurium class Ib ribonucleotide reductase determined by high field EPR of R2F single crystals.
  J Biol Chem, 281, 31743-31752.  
17176061 M.H.Sazinsky, P.W.Dunten, M.S.McCormick, A.DiDonato, and S.J.Lippard (2006).
X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase.
  Biochemistry, 45, 15392-15404.
PDB codes: 2inn 2inp
16756507 P.Nordlund, and P.Reichard (2006).
Ribonucleotide reductases.
  Annu Rev Biochem, 75, 681-706.  
16322104 E.Torrents, M.Sahlin, D.Biglino, A.Gräslund, and B.M.Sjöberg (2005).
Efficient growth inhibition of Bacillus anthracis by knocking out the ribonucleotide reductase tyrosyl radical.
  Proc Natl Acad Sci U S A, 102, 17946-17951.  
15240491 D.A.Svistunenko, and C.E.Cooper (2004).
A new method of identifying the site of tyrosyl radicals in proteins.
  Biophys J, 87, 582-595.  
15322079 K.R.Strand, S.Karlsen, M.Kolberg, A.K.Røhr, C.H.Görbitz, and K.K.Andersson (2004).
Crystal structural studies of changes in the native dinuclear iron center of ribonucleotide reductase protein R2 from mouse.
  J Biol Chem, 279, 46794-46801.
PDB codes: 1w68 1w69
15087448 R.Schwarzenbacher, F.Stenner-Liewen, H.Liewen, H.Robinson, H.Yuan, E.Bossy-Wetzel, J.C.Reed, and R.C.Liddington (2004).
Structure of the Chlamydia protein CADD reveals a redox enzyme that modulates host cell apoptosis.
  J Biol Chem, 279, 29320-29324.
PDB code: 1rcw
15211525 R.Schwarzenbacher, F.Stenner-Liewen, H.Liewen, J.C.Reed, and R.C.Liddington (2004).
Crystal structure of PqqC from Klebsiella pneumoniae at 2.1 A resolution.
  Proteins, 56, 401-403.  
12767114 B.S.Cooperman (2003).
Oligopeptide inhibition of class I ribonucleotide reductases.
  Biopolymers, 71, 117-131.  
12777781 M.Uppsten, M.Färnegårdh, A.Jordan, S.Ramaswamy, and U.Uhlin (2003).
Expression and preliminary crystallographic studies of R1E, the large subunit of ribonucleotide reductase from Salmonella typhimurium.
  Acta Crystallogr D Biol Crystallogr, 59, 1081-1083.  
10449377 C.M.Summa, A.Lombardi, M.Lewis, and W.F.DeGrado (1999).
Tertiary templates for the design of diiron proteins.
  Curr Opin Struct Biol, 9, 500-508.  
10423453 M.Bolognesi, C.Rosano, R.Losso, A.Borassi, M.Rizzi, J.B.Wittenberg, A.Boffi, and P.Ascenzi (1999).
Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study.
  Biophys J, 77, 1093-1099.
PDB codes: 1b0b 1ebc 1ebt
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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