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

 

 

 

 

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Contents
Protein chains
642 a.a. *
149 a.a. *
Ligands
FAD ×2
SF4 ×4
Waters ×1111
* Residue conservation analysis
PDB id:
2fje
Name: Oxidoreductase
Title: Adenosine-5-phosphosulfate reductase oxidized state
Structure: Adenylylsulfate reductase, subunit a. Chain: a, c. Synonym: apra. Adenylylsulfate reductase, subunit b. Chain: b, d. Synonym: aprb. Ec: 1.8.99.2
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Organism_taxid: 2234
Biol. unit: Tetramer (from PQS)
Resolution:
1.80Å     R-factor:   0.166     R-free:   0.192
Authors: A.Schiffer,G.Fritz,P.M.Kroneck,U.Ermler
Key ref:
A.Schiffer et al. (2006). Reaction mechanism of the iron-sulfur flavoenzyme adenosine-5'-phosphosulfate reductase based on the structural characterization of different enzymatic states. Biochemistry, 45, 2960-2967. PubMed id: 16503650 DOI: 10.1021/bi0521689
Date:
02-Jan-06     Release date:   28-Mar-06    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
O28603  (O28603_ARCFU) -  Adenylylsulfate reductase, subunit A (AprA) from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		 
Seq:
Struc: 		643 a.a.
642 a.a.
Protein chains
Pfam   ArchSchema ?
O28604  (O28604_ARCFU) -  Adenylylsulfate reductase, subunit B (AprB) from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		150 a.a.
149 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, C, B, D: E.C.1.8.99.2  - adenylyl-sulfate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: sulfite + A + AMP + 2 H+ = adenosine 5'-phosphosulfate + AH2
sulfite
 +
+ AMP
 + 2 × H(+)
 = adenosine 5'-phosphosulfate
 + AH2
      Cofactor: FAD; Fe cation
FAD
Bound ligand (Het Group name = FAD) corresponds exactly 		Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/bi0521689 Biochemistry 45:2960-2967 (2006)
PubMed id: 16503650  
 
 
Reaction mechanism of the iron-sulfur flavoenzyme adenosine-5'-phosphosulfate reductase based on the structural characterization of different enzymatic states.
A.Schiffer, G.Fritz, P.M.Kroneck, U.Ermler.
 
  ABSTRACT  
 
The iron-sulfur flavoenzyme adenosine-5'-phosphosulfate (APS) reductase catalyzes a key reaction of the global sulfur cycle by reversibly transforming APS to sulfite and AMP. The structures of the dissimilatory enzyme from Archaeoglobus fulgidus in the reduced state (FAD(red)) and in the sulfite adduct state (FAD-sulfite-AMP) have been recently elucidated at 1.6 and 2.5 A resolution, respectively. Here we present new structural features of the enzyme trapped in four different catalytically relevant states that provide us with a detailed picture of its reaction cycle. In the oxidized state (FAD(ox)), the isoalloxazine moiety of the FAD cofactor exhibits a similarly bent conformation as observed in the structure of the reduced enzyme. In the APS-bound state (FAD(ox)-APS), the substrate APS is embedded into a 17 A long substrate channel in such a way that the isoalloxazine ring is pushed toward the channel bottom, thereby producing a compressed enzyme-substrate complex. A clamp formed by residues ArgA317 and LeuA278 to fix the adenine ring and the curved APS conformation appear to be key factors to hold APS in a strained conformation. This energy-rich state is relaxed during the attack of APS on the reduced FAD. A relaxed FAD-sulfite adduct is observed in the structure of the FAD-sulfite state. Finally, a FAD-sulfite-AMP1 state with AMP within van der Waals distance of the sulfite adduct could be characterized. This structure documents how adjacent negative charges are stabilized by the protein matrix which is crucial for forming APS from AMP and sulfite in the reverse reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19820092 Y.L.Chiang, Y.C.Hsieh, J.Y.Fang, E.H.Liu, Y.C.Huang, P.Chuankhayan, J.Jeyakanthan, M.Y.Liu, S.I.Chan, and C.J.Chen (2009).
Crystal structure of Adenylylsulfate reductase from Desulfovibrio gigas suggests a potential self-regulation mechanism involving the C terminus of the beta-subunit.
  J Bacteriol, 191, 7597-7608.
PDB code: 3gyx
18231600 B.Meyer, and J.Kuever (2008).
Homology Modeling of Dissimilatory APS Reductases (AprBA) of Sulfur-Oxidizing and Sulfate-Reducing Prokaryotes.
  PLoS ONE, 3, e1514.  
  18997328 H.Ogata, A.Goenka Agrawal, A.P.Kaur, R.Goddard, W.Gärtner, and W.Lubitz (2008).
Purification, crystallization and preliminary X-ray analysis of adenylylsulfate reductase from Desulfovibrio vulgaris Miyazaki F.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1010-1012.  
18190525 N.G.Leferink, W.A.van den Berg, and W.J.van Berkel (2008).
l-Galactono-gamma-lactone dehydrogenase from Arabidopsis thaliana, a flavoprotein involved in vitamin C biosynthesis.
  FEBS J, 275, 713-726.  
17303759 T.Sato, H.Atomi, and T.Imanaka (2007).
Archaeal type III RuBisCOs function in a pathway for AMP metabolism.
  Science, 315, 1003-1006.  
17070680 L.De Colibus, and A.Mattevi (2006).
New frontiers in structural flavoenzymology.
  Curr Opin Struct Biol, 16, 722-728.  
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 code is shown on the right.

 

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