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PDBsum entry 1ycf

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1ycf
Jmol
Contents
Protein chains
398 a.a. *
Ligands
FEO-OXY ×3
FMN ×4
FEO
OXY
Metals
_ZN ×3
Waters ×61
* Residue conservation analysis
PDB id:
1ycf
Name: Oxidoreductase
Title: Oxidized (di-ferric) fpra from moorella thermoacetica
Structure: Nitric oxide reductase. Chain: a, b, c, d. Fragment: di-iron nitric oxide reductase. Synonym: type a flavoprotein fpra, fmn- protein fpra, flavoprotein a. Engineered: yes
Source: Moorella thermoacetica. Organism_taxid: 1525. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
3.00Å     R-factor:   0.217     R-free:   0.260
Authors: R.Silaghi-Dumitrescu,D.M.Kurtz,W.N.Lanzilotta
Key ref:
R.Silaghi-Dumitrescu et al. (2005). X-ray crystal structures of Moorella thermoacetica FprA. Novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase. Biochemistry, 44, 6492-6501. PubMed id: 15850383 DOI: 10.1021/bi0473049
Date:
22-Dec-04     Release date:   19-Apr-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9FDN7  (FPRA_MOOTA) -  Nitric oxide reductase
Seq:
Struc:
399 a.a.
398 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     5 terms  

 

 
DOI no: 10.1021/bi0473049 Biochemistry 44:6492-6501 (2005)
PubMed id: 15850383  
 
 
X-ray crystal structures of Moorella thermoacetica FprA. Novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase.
R.Silaghi-Dumitrescu, D.M.Kurtz, L.G.Ljungdahl, W.N.Lanzilotta.
 
  ABSTRACT  
 
Several members of a widespread class of bacterial and archaeal metalloflavoproteins, called FprA, likely function as scavenging nitric oxide reductases (S-NORs). However, the only published X-ray crystal structure of an FprA is for a protein characterized as a rubredoxin:dioxygen oxidoreductase (ROO) from Desulfovibrio gigas. Therefore, the crystal structure of Moorella thermoacetica FprA, which has been established to function as an S-NOR, was solved in three different states: as isolated, reduced, and reduced, NO-reacted. As is the case for D. gigas ROO, the M. thermoacetica FprA contains a solvent-bridged non-heme, non-sulfur diiron site with five-coordinate iron centers bridged by an aspartate, and terminal glutamate, aspartate, and histidine ligands. However, the M. thermoacetica FprA diiron site showed four His ligands, two to each iron, in all three states, whereas the D. gigas ROO diiron site was reported to contain only three His ligands, even though the fourth His residue is conserved. The Fe1-Fe2 distance within the diiron site of M. thermoacetica FprA remained at 3.2-3.4 A with little or no movement of the protein ligands in the three different states and with conservation of the two proximal open coordination sites. Molecular modeling indicated that each open coordination site can accommodate an end-on NO. This relatively rigid and symmetrical diiron site structure is consistent with formation of a diferrous dinitrosyl as the committed catalytic intermediate leading to formation of N(2)O. These results provide new insight into the structural features that fine-tune biological non-heme diiron sites for dioxygen activation vs nitric oxide reduction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20414806 R.S.Gupta (2010).
Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups.
  Photosynth Res, 104, 357-372.  
19337761 B.L.Victor, A.M.Baptista, and C.M.Soares (2009).
Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas.
  J Biol Inorg Chem, 14, 853-862.  
19084524 F.Hillmann, O.Riebe, R.J.Fischer, A.Mot, J.D.Caranto, D.M.Kurtz, and H.Bahl (2009).
Reductive dioxygen scavenging by flavo-diiron proteins of Clostridium acetobutylicum.
  FEBS Lett, 583, 241-245.  
19156270 R.Wang, M.A.Camacho-Fernandez, W.Xu, J.Zhang, and L.Li (2009).
Neutral and reduced Roussin's red salt ester [Fe(2)(mu-RS)(2)(NO)(4)] (R = n-Pr, t-Bu, 6-methyl-2-pyridyl and 4,6-dimethyl-2-pyrimidyl): synthesis, X-ray crystal structures, spectroscopic, electrochemical and density functional theoretical investigations.
  Dalton Trans, (), 777-786.  
18077462 A.Di Matteo, F.M.Scandurra, F.Testa, E.Forte, P.Sarti, M.Brunori, and A.Giuffrè (2008).
The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis.
  J Biol Chem, 283, 4061-4068.
PDB code: 2q9u
18786405 M.V.Petoukhov, J.B.Vicente, P.B.Crowley, M.A.Carrondo, M.Teixeira, and D.I.Svergun (2008).
Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering.
  Structure, 16, 1428-1436.  
17480207 H.Seedorf, C.H.Hagemeier, S.Shima, R.K.Thauer, E.Warkentin, and U.Ermler (2007).
Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O.
  FEBS J, 274, 1588-1599.
PDB codes: 2ohh 2ohi 2ohj
17181540 J.B.Vicente, F.M.Scandurra, J.V.Rodrigues, M.Brunori, P.Sarti, M.Teixeira, and A.Giuffrè (2007).
Kinetics of electron transfer from NADH to the Escherichia coli nitric oxide reductase flavorubredoxin.
  FEBS J, 274, 677-686.  
16957917 L.M.Blomberg, M.R.Blomberg, and P.E.Siegbahn (2007).
Theoretical study of the reduction of nitric oxide in an A-type flavoprotein.
  J Biol Inorg Chem, 12, 79-89.  
17318598 M.A.Carrondo, I.Bento, P.M.Matias, and P.F.Lindley (2007).
Crystallographic evidence for dioxygen interactions with iron proteins.
  J Biol Inorg Chem, 12, 429-442.  
17534533 P.Moënne-Loccoz (2007).
Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins.
  Nat Prod Rep, 24, 610-620.  
16494475 J.P.Collman, Y.L.Yan, J.Lei, and P.H.Dinolfo (2006).
Efficient synthesis of trisimidazole and glutaric acid bearing porphyrins: ligands for active-site models of bacterial nitric oxide reductase.
  Org Lett, 8, 923-926.  
16100392 J.B.Vicente, and M.Teixeira (2005).
Redox and spectroscopic properties of the Escherichia coli nitric oxide-detoxifying system involving flavorubredoxin and its NADH-oxidizing redox partner.
  J Biol Chem, 280, 34599-34608.  
16332833 S.Kawasaki, Y.Watamura, M.Ono, T.Watanabe, K.Takeda, and Y.Niimura (2005).
Adaptive responses to oxygen stress in obligatory anaerobes Clostridium acetobutylicum and Clostridium aminovalericum.
  Appl Environ Microbiol, 71, 8442-8450.  
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.