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PDBsum entry 1asp
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1asp

 

 

 

 

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Contents
Protein chains
552 a.a. *
Ligands
NAG ×2
_OH ×2
PEO ×2
Metals
_CU ×9
Waters ×967
* Residue conservation analysis
PDB id:
1asp
Name: Oxidoreductase
Title: X-ray structures and mechanistic implications of three functional derivatives of ascorbate oxidase from zucchini: reduced-, peroxide-, and azide-forms
Structure: Ascorbate oxidase. Chain: a, b. Engineered: yes
Source: Cucurbita pepo var. Melopepo. Zucchini. Organism_taxid: 3665. Strain: var. Melopepo
Biol. unit: Dimer (from PQS)
Resolution:
2.59Å     R-factor:   0.160    
Authors: A.Messerschmidt,H.Luecke,R.Huber
Key ref: A.Messerschmidt et al. (1993). X-ray structures and mechanistic implications of three functional derivatives of ascorbate oxidase from zucchini. Reduced, peroxide and azide forms. J Mol Biol, 230, 997. PubMed id: 8478945
Date:
25-Nov-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P37064  (ASO_CUCPM) -  L-ascorbate oxidase from Cucurbita pepo var. melopepo
Seq:
Struc: 		 
Seq:
Struc: 		552 a.a.
553 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.10.3.3  - L-ascorbate oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 L-ascorbate + O2 = 4 monodehydro-L-ascorbate radical + 2 H2O
4 × L-ascorbate
Bound ligand (Het Group name = NAG)
matches with 62.50% similarity 		+
O2
Bound ligand (Het Group name = PEO)
corresponds exactly 		= 4 × monodehydro-L-ascorbate radical
 + 2 × H2O
      Cofactor: Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
J Mol Biol 230:997 (1993)
PubMed id: 8478945  
 
 
X-ray structures and mechanistic implications of three functional derivatives of ascorbate oxidase from zucchini. Reduced, peroxide and azide forms.
A.Messerschmidt, H.Luecke, R.Huber.
 
  ABSTRACT  
 
The X-ray structures of three functional derivatives of ascorbate oxidase (EC 1.10.3.3) from Zucchini have been determined and are compared to the "native" oxidized form. The fully reduced form of ascorbate oxidase has been refined to a crystallographic R-factor of 19.6% for all reflections between 8.0 A and 2.2 A resolution. The geometry at the type-1 copper (CU1) is unchanged compared to the oxidized form, but the oxygen ligand bridging the copper ions CU2 and CU3 (spectroscopic type-3 copper pair) is released and the copper ions move apart yielding a trigonal planar co-ordination with their ligating histidine residues. The co-ordination at the copper ion CU4 (spectroscopic type-2 copper) is not affected. The copper-copper distances increase from an average 3.7 A in the native form to 5.1 A for CU2-CU3, 4.4 A for CU2-CU4 and 4.1 A for CU3-CU4. The peroxide derivative of ascorbate oxidase has been refined to a crystallographic R-factor of 16.0% for all reflections between 8.0 A and 2.59 A resolution. The geometry at the type-1 copper site is not changed compared to the oxidized form. The oxygen ligand bridging copper atoms CU2 and CU3 is lost, too. The peroxide binds terminally to the copper ion CU2 as hydroperoxide. Copper ion CU2 is fourfold co-ordinated to the NE2 atoms of the three histidine residues and to the oxygen atom of the terminally bound peroxide molecule in a distorted tetrahedral geometry. Copper ion CU3 is threefold co-ordinated as in the reduced form and co-ordination around copper atom CU4 is unaltered. The copper-copper distances increase to 4.8 A for CU2-CU3 and 4.5 A for CU2-CU4. The distance CU3-CU4 remains 3.7 A. Treatment with peroxide causes a partial depletion of copper ion CU2. The refinement for the azide derivative of ascorbate oxidase converged at a crystallographic R-factor of 17.8% for all reflections between 8.0 A and 2.32 A. There are no significant structural changes at the type-1 copper site. The oxygen ligand bridging copper ions CU2 and CU3 is again released. Two azide molecules bind terminally to copper ion CU2. Copper ion CU2 is fivefold co-ordinated to the NE2 atoms of the three histidine residues and to both terminally bound azide molecules in a trigonal-bipyramidal manner. Copper-copper distances increase to 5.1 A for CU2-CU3 and 4.6 A for CU2-CU4. The distance CU3-CU4 is decreased to 3.6 A.(ABSTRACT TRUNCATED AT 400 WORDS)
 

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.
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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.
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19701722 M.B.Rajasekaran, S.Nilapwar, S.C.Andrews, and K.A.Watson (2010).
EfeO-cupredoxins: major new members of the cupredoxin superfamily with roles in bacterial iron transport.
  Biometals, 23, 1.  
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.  
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
19030628 A.Beheshti, W.Clegg, V.Nobakht, M.Panahi Mehr, and L.Russo (2008).
Complexes of copper(I) and silver(I) with bis(methimazolyl)borate and dihydrobis(2-mercaptothiazolyl)borate ligands.
  Dalton Trans, (), 6641-6646.  
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.  
17918839 J.Yoon, and E.I.Solomon (2007).
Electronic structure of the peroxy intermediate and its correlation to the native intermediate in the multicopper oxidases: insights into the reductive cleavage of the o-o bond.
  J Am Chem Soc, 129, 13127-13136.  
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
17011183 A.C.Rosenzweig, and M.H.Sazinsky (2006).
Structural insights into dioxygen-activating copper enzymes.
  Curr Opin Struct Biol, 16, 729-735.  
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.  
16230618 A.B.Taylor, C.S.Stoj, L.Ziegler, D.J.Kosman, and P.J.Hart (2005).
The copper-iron connection in biology: structure of the metallo-oxidase Fet3p.
  Proc Natl Acad Sci U S A, 102, 15459-15464.
PDB code: 1zpu
16231129 G.Battistuzzi, M.Bellei, A.Leonardi, R.Pierattelli, A.De Candia, A.J.Vila, and M.Sola (2005).
Reduction thermodynamics of the T1 Cu site in plant and fungal laccases.
  J Biol Inorg Chem, 10, 867-873.  
16234932 I.Bento, L.O.Martins, G.Gato Lopes, M.Arménia Carrondo, and P.F.Lindley (2005).
Dioxygen reduction by multi-copper oxidases; a structural perspective.
  Dalton Trans, (), 3507-3513.
PDB codes: 1w6l 1w6w 1w8e 2bhf
16471062 I.Gautier-Luneau, D.Phanon, C.Duboc, D.Luneau, and J.L.Pierre (2005).
Electron delocalisation in a trinuclear copper(II) complex: high-field EPR characterization and magnetic properties of Na3[Cu3(mal)3(H2O)] x 8H2O.
  Dalton Trans, (), 3795-3799.  
14764581 F.J.Enguita, D.Marçal, L.O.Martins, R.Grenha, A.O.Henriques, P.F.Lindley, and M.A.Carrondo (2004).
Substrate and dioxygen binding to the endospore coat laccase from Bacillus subtilis.
  J Biol Chem, 279, 23472-23476.
PDB codes: 1hkz 1uvw 3zdw
15006640 L.Santagostini, M.Gullotti, L.De Gioia, P.Fantucci, E.Franzini, A.Marchesini, E.Monzani, and L.Casella (2004).
Probing the location of the substrate binding site of ascorbate oxidase near type 1 copper: an investigation through spectroscopic, inhibition and docking studies.
  Int J Biochem Cell Biol, 36, 881-892.  
12794343 A.J.Blake, P.Hubberstey, A.D.Mackrell, and C.Wilson (2003).
3,6-Dichloro-4-[2-(4-thiamorpholino)ethanesulfanyl]pyridazine and 3,6-bis(pyrazol-1-yl)-4-[2-(4-thiamorpholino)ethanesulfanyl]pyridazine.
  Acta Crystallogr C, 59, o293-o297.  
12637519 F.J.Enguita, L.O.Martins, A.O.Henriques, and M.A.Carrondo (2003).
Crystal structure of a bacterial endospore coat component. A laccase with enhanced thermostability properties.
  J Biol Chem, 278, 19416-19425.
PDB code: 1gsk
12198312 F.J.Enguita, P.M.Matias, L.O.Martins, D.Plácido, A.O.Henriques, and M.A.Carrondo (2002).
Spore-coat laccase CotA from Bacillus subtilis: crystallization and preliminary X-ray characterization by the MAD method.
  Acta Crystallogr D Biol Crystallogr, 58, 1490-1493.  
12118243 N.Hakulinen, L.L.Kiiskinen, K.Kruus, M.Saloheimo, A.Paananen, A.Koivula, and J.Rouvinen (2002).
Crystal structure of a laccase from Melanocarpus albomyces with an intact trinuclear copper site.
  Nat Struct Biol, 9, 601-605.
PDB code: 1gw0
12044164 T.Bertrand, C.Jolivalt, P.Briozzo, E.Caminade, N.Joly, C.Madzak, and C.Mougin (2002).
Crystal structure of a four-copper laccase complexed with an arylamine: insights into substrate recognition and correlation with kinetics.
  Biochemistry, 41, 7325-7333.
PDB code: 1kya
11411987 R.Wegner, M.Gottschaldt, H.Görls, E.G.Jäger, and D.Klemm (2001).
Copper(II) complexes of aminocarbohydrate beta-ketoenaminic ligands: efficient catalysts in catechol oxidation.
  Chemistry, 7, 2143-2157.  
10771420 M.J.Fei, E.Yamashita, N.Inoue, M.Yao, H.Yamaguchi, T.Tsukihara, K.Shinzawa-Itoh, R.Nakashima, and S.Yoshikawa (2000).
X-ray structure of azide-bound fully oxidized cytochrome c oxidase from bovine heart at 2.9 A resolution.
  Acta Crystallogr D Biol Crystallogr, 56, 529-535.  
10694398 N.J.Blackburn, M.Ralle, R.Hassett, and D.J.Kosman (2000).
Spectroscopic analysis of the trinuclear cluster in the Fet3 protein from yeast, a multinuclear copper oxidase.
  Biochemistry, 39, 2316-2324.  
10504390 G.Musci, G.C.Bellenchi, and L.Calabrese (1999).
The multifunctional oxidase activity of ceruloplasmin as revealed by anion binding studies.
  Eur J Biochem, 265, 589-597.  
10551829 H.Huang, G.Zoppellaro, and T.Sakurai (1999).
Spectroscopic and kinetic studies on the oxygen-centered radical formed during the four-electron reduction process of dioxygen by Rhus vernicifera laccase.
  J Biol Chem, 274, 32718-32724.  
10583375 I.Gromov, A.Marchesini, O.Farver, I.Pecht, and D.Goldfarb (1999).
Azide binding to the trinuclear copper center in laccase and ascorbate oxidase.
  Eur J Biochem, 266, 820-830.  
10320665 J.Torres, and M.T.Wilson (1999).
The reactions of copper proteins with nitric oxide.
  Biochim Biophys Acta, 1411, 310-322.  
10226045 M.A.McGuirl, and D.M.Dooley (1999).
Copper-containing oxidases.
  Curr Opin Chem Biol, 3, 138-144.  
9858779 K.Takeda, H.Itoh, I.Yoshioka, M.Yamamoto, H.Misaki, S.Kajita, K.Shirai, M.Kato, T.Shin, S.Murao, and N.Tsukagoshi (1998).
Cloning of a thermostable ascorbate oxidase gene from Acremonium sp. HI-25 and modification of the azide sensitivity of the enzyme by site-directed mutagenesis.
  Biochim Biophys Acta, 1388, 444-456.  
9722559 R.F.Hassett, D.S.Yuan, and D.J.Kosman (1998).
Spectral and kinetic properties of the Fet3 protein from Saccharomyces cerevisiae, a multinuclear copper ferroxidase enzyme.
  J Biol Chem, 273, 23274-23282.  
9624044 S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, and T.Tsukihara (1998).
Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.
  Science, 280, 1723-1729.
PDB codes: 1oco 1ocr 1ocz 2occ
9266714 G.Alzuet, L.Bubacco, L.Casella, G.P.Rocco, B.Salvato, and M.Beltramini (1997).
The binding of azide to copper-containing and cobalt-containing forms of hemocyanin from the mediterranean crab Carcinus aestuarii.
  Eur J Biochem, 247, 688-694.  
9125505 S.Gaspard, E.Monzani, L.Casella, M.Gullotti, S.Maritano, and A.Marchesini (1997).
Inhibition of ascorbate oxidase by phenolic compounds. Enzymatic and spectroscopic studies.
  Biochemistry, 36, 4852-4859.  
8534676 B.C.Berks, S.J.Ferguson, J.W.Moir, and D.J.Richardson (1995).
Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions.
  Biochim Biophys Acta, 1232, 97.  
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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