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PDBsum entry 2bhf
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Oxidoreductase PDB id
2bhf

 

 

 

 

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Contents
Protein chain
504 a.a. *
Ligands
GOL ×3
Metals
CU1 ×4
Waters ×300
* Residue conservation analysis
PDB id:
2bhf
Name: Oxidoreductase
Title: 3d structure of the reduced form of cota
Structure: Spore coat protein a. Chain: a. Synonym: cota. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.50Å     R-factor:   0.175     R-free:   0.213
Authors: I.Bento,L.O.Martins,G.G.Lopes,M.A.Carrondo,P.F.Lindley
Key ref: I.Bento et al. (2005). Dioxygen reduction by multi-copper oxidases; a structural perspective. Dalton Trans, 21, 3507-3513. PubMed id: 16234932
Date:
10-Jan-05     Release date:   26-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07788  (COTA_BACSU) -  Laccase from Bacillus subtilis (strain 168)
Seq:
Struc: 		513 a.a.
504 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.1.10.3.2  - laccase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 hydroquinone + O2 = 4 benzosemiquinone + 2 H2O
4 × hydroquinone
 + O2
 = 4 × benzosemiquinone
 + 2 × H2O
      Cofactor: Cu cation
   Enzyme class 2: E.C.1.3.3.5  - bilirubin oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: 2 (4Z,15Z)-bilirubin IXalpha + O2 = 2 biliverdin IXalpha + 2 H2O
2 × (4Z,15Z)-bilirubin IXalpha
 + O2
 = 2 × biliverdin IXalpha
 + 2 × H2O
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Dalton Trans 21:3507-3513 (2005)
PubMed id: 16234932  
 
 
Dioxygen reduction by multi-copper oxidases; a structural perspective.
I.Bento, L.O.Martins, G.Gato Lopes, M.Arménia Carrondo, P.F.Lindley.
 
  ABSTRACT  
 
The multi-copper oxidases oxidise substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. The precise mechanism of this reduction has been unclear, but recent X-ray structural studies using the CotA endospore coat protein from Bacillus subtilis have given further insights into the principal stages. It is proposed that the mechanism involves binding of the dioxygen into the trinuclear centre so that it is sited approximately symmetrically between the two type 3 copper ions with one oxygen atom close to the type 2 copper ion. Further stages involve the formation of a peroxide intermediate and following the splitting of this intermediate, the migration of the hydroxide moieties towards the solvent exit channel. The migration steps are likely to involve a movement of the type 2 copper ion and its environment. Details of a putative mechanism are described herein based both on structures already reported in the literature and on structures of the CotA protein in the oxidised and reduced states and with the addition of peroxide and the inhibitor, azide.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21298193 F.G.Mutti, M.Gullotti, L.Casella, L.Santagostini, R.Pagliarin, K.K.Andersson, M.F.Iozzi, and G.Zoppellaro (2011).
A new chiral, poly-imidazole N8-ligand and the related di- and tri-copper(II) complexes: synthesis, theoretical modelling, spectroscopic properties, and biomimetic stereoselective oxidations.
  Dalton Trans, 40, 5436-5457.  
21258722 Y.J.Choi, K.B.Cho, M.Kubo, T.Ogura, K.D.Karlin, J.Cho, and W.Nam (2011).
Spectroscopic and computational characterization of Cu(II)-OOR (R = H or cumyl) complexes bearing a Me(6)-tren ligand.
  Dalton Trans, 40, 2234-2241.  
20377263 A.J.Augustine, C.Kjaergaard, M.Qayyum, L.Ziegler, D.J.Kosman, K.O.Hodgson, B.Hedman, and E.I.Solomon (2010).
Systematic perturbation of the trinuclear copper cluster in the multicopper oxidases: the role of active site asymmetry in its reduction of O2 to H2O.
  J Am Chem Soc, 132, 6057-6067.  
20597980 A.T.Fernandes, J.M.Damas, S.Todorovic, R.Huber, M.C.Baratto, R.Pogni, C.M.Soares, and L.O.Martins (2010).
The multicopper oxidase from the archaeon Pyrobaculum aerophilum shows nitrous oxide reductase activity.
  FEBS J, 277, 3176-3189.  
20200715 Z.Chen, P.Durão, C.S.Silva, M.M.Pereira, S.Todorovic, P.Hildebrandt, I.Bento, P.F.Lindley, and L.O.Martins (2010).
The role of Glu498 in the dioxygen reactivity of CotA-laccase from Bacillus subtilis.
  Dalton Trans, 39, 2875-2882.
PDB codes: 4ako 4akp 4akq
19346471 J.Yoon, S.Fujii, and E.I.Solomon (2009).
Geometric and electronic structure differences between the type 3 copper sites of the multicopper oxidases and hemocyanin/tyrosinase.
  Proc Natl Acad Sci U S A, 106, 6585-6590.  
19465775 K.M.Polyakov, T.V.Fedorova, E.V.Stepanova, E.A.Cherkashin, S.A.Kurzeev, B.V.Strokopytov, V.S.Lamzin, and O.V.Koroleva (2009).
Structure of native laccase from Trametes hirsuta at 1.8 A resolution.
  Acta Crystallogr D Biol Crystallogr, 65, 611-617.  
19780817 M.Andberg, N.Hakulinen, S.Auer, M.Saloheimo, A.Koivula, J.Rouvinen, and K.Kruus (2009).
Essential role of the C-terminus in Melanocarpus albomyces laccase for enzyme production, catalytic properties and structure.
  FEBS J, 276, 6285-6300.
PDB code: 3dkh
19224923 T.J.Lawton, L.A.Sayavedra-Soto, D.J.Arp, and A.C.Rosenzweig (2009).
Crystal structure of a two-domain multicopper oxidase: IMPLICATIONS FOR THE EVOLUTION OF MULTICOPPER BLUE PROTEINS.
  J Biol Chem, 284, 10174-10180.
PDB code: 3g5w
18292878 M.A.Tadesse, A.D'Annibale, C.Galli, P.Gentili, and F.Sergi (2008).
An assessment of the relative contributions of redox and steric issues to laccase specificity towards putative substrates.
  Org Biomol Chem, 6, 868-878.  
17957391 P.Durão, Z.Chen, A.T.Fernandes, P.Hildebrandt, D.H.Murgida, S.Todorovic, M.M.Pereira, E.P.Melo, and L.O.Martins (2008).
Copper incorporation into recombinant CotA laccase from Bacillus subtilis: characterization of fully copper loaded enzymes.
  J Biol Inorg Chem, 13, 183-193.  
17918838 A.J.Augustine, L.Quintanar, C.S.Stoj, D.J.Kosman, and E.I.Solomon (2007).
Spectroscopic and kinetic studies of perturbed trinuclear copper clusters: the role of protons in reductive cleavage of the O-O bond in the multicopper oxidase Fet3p.
  J Am Chem Soc, 129, 13118-13126.  
17622421 E.C.Brown, B.Johnson, S.Palavicini, B.E.Kucera, L.Casella, and W.B.Tolman (2007).
Modular syntheses of multidentate ligands with variable N-donors: applications to tri- and tetracopper(I) complexes.
  Dalton Trans, (), 3035-3042.  
17242517 I.Bento, C.Peixoto, V.N.Zaitsev, and P.F.Lindley (2007).
Ceruloplasmin revisited: structural and functional roles of various metal cation-binding sites.
  Acta Crystallogr D Biol Crystallogr, 63, 240-248.
PDB code: 2j5w
17702865 J.Yoon, B.D.Liboiron, R.Sarangi, K.O.Hodgson, B.Hedman, and E.I.Solomon (2007).
The two oxidized forms of the trinuclear Cu cluster in the multicopper oxidases and mechanism for the decay of the native intermediate.
  Proc Natl Acad Sci U S A, 104, 13609-13614.  
17897461 M.Ferraroni, N.M.Myasoedova, V.Schmatchenko, A.A.Leontievsky, L.A.Golovleva, A.Scozzafava, and F.Briganti (2007).
Crystal structure of a blue laccase from Lentinus tigrinus: evidences for intermediates in the molecular oxygen reductive splitting by multicopper oxidases.
  BMC Struct Biol, 7, 60.
PDB code: 2qt6
18021071 O.V.Morozova, G.P.Shumakovich, M.A.Gorbacheva, S.V.Shleev, and A.I.Yaropolov (2007).
"Blue" laccases.
  Biochemistry (Mosc), 72, 1136-1150.  
17011183 A.C.Rosenzweig, and M.H.Sazinsky (2006).
Structural insights into dioxygen-activating copper enzymes.
  Curr Opin Struct Biol, 16, 729-735.  
16944230 A.V.Lyashenko, I.Bento, V.N.Zaitsev, N.E.Zhukhlistova, Y.N.Zhukova, A.G.Gabdoulkhakov, E.Y.Morgunova, W.Voelter, G.S.Kachalova, E.V.Stepanova, O.V.Koroleva, V.S.Lamzin, V.I.Tishkov, C.Betzel, P.F.Lindley, and A.M.Mikhailov (2006).
X-ray structural studies of the fungal laccase from Cerrena maxima.
  J Biol Inorg Chem, 11, 963-973.  
  17012782 A.V.Lyashenko, N.E.Zhukhlistova, A.G.Gabdoulkhakov, Y.N.Zhukova, W.Voelter, V.N.Zaitsev, I.Bento, E.V.Stepanova, G.S.Kachalova, O.V.Koroleva, E.A.Cherkashyn, V.I.Tishkov, V.S.Lamzin, K.Schirwitz, E.Y.Morgunova, C.Betzel, P.F.Lindley, and A.M.Mikhailov (2006).
Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 954-957.
PDB code: 2h5u
16791638 I.Bento, M.A.Carrondo, and P.F.Lindley (2006).
Reduction of dioxygen by enzymes containing copper.
  J Biol Inorg Chem, 11, 539-547.  
16680453 P.Durão, I.Bento, A.T.Fernandes, E.P.Melo, P.F.Lindley, and L.O.Martins (2006).
Perturbations of the T1 copper site in the CotA laccase from Bacillus subtilis: structural, biochemical, enzymatic and stability studies.
  J Biol Inorg Chem, 11, 514-526.  
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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