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PDBsum entry 1w9y

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Oxygenase PDB id
1w9y
Jmol
Contents
Protein chain
299 a.a. *
Ligands
SO4
Waters ×95
* Residue conservation analysis
PDB id:
1w9y
Name: Oxygenase
Title: The structure of acc oxidase
Structure: 1-aminocyclopropane-1-carboxylate oxidase 1. Chain: a. Synonym: acc oxidase 1, ethylene-forming enzyme, efe. Engineered: yes
Source: Petunia hybrida. Petunia. Organism_taxid: 4102. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.10Å     R-factor:   0.223     R-free:   0.292
Authors: Z.Zhang,J.-S.Ren,I.J.Clifton,C.J.Schofield
Key ref:
Z.Zhang et al. (2004). Crystal structure and mechanistic implications of 1-aminocyclopropane-1-carboxylic acid oxidase--the ethylene-forming enzyme. Chem Biol, 11, 1383-1394. PubMed id: 15489165 DOI: 10.1016/j.chembiol.2004.08.012
Date:
20-Oct-04     Release date:   26-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q08506  (ACCO1_PETHY) -  1-aminocyclopropane-1-carboxylate oxidase 1
Seq:
Struc:
319 a.a.
299 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.17.4  - Aminocyclopropanecarboxylate oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Ethylene Biosynthesis
      Reaction: 1-aminocyclopropane-1-carboxylate + ascorbate + O2 = ethylene + cyanide + dehydroascorbate + CO2 + 2 H2O
1-aminocyclopropane-1-carboxylate
+ ascorbate
+ O(2)
= ethylene
+ cyanide
+ dehydroascorbate
+ CO(2)
+ 2 × H(2)O
      Cofactor: Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.chembiol.2004.08.012 Chem Biol 11:1383-1394 (2004)
PubMed id: 15489165  
 
 
Crystal structure and mechanistic implications of 1-aminocyclopropane-1-carboxylic acid oxidase--the ethylene-forming enzyme.
Z.Zhang, J.S.Ren, I.J.Clifton, C.J.Schofield.
 
  ABSTRACT  
 
The final step in the biosynthesis of the plant signaling molecule ethylene is catalyzed by 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO). ACCO requires bicarbonate as an activator and catalyzes the oxidation of ACC to give ethylene, CO2, and HCN. We report crystal structures of ACCO in apo-form (2.1 A resolution) and complexed with Fe(II) (2.55 A) or Co(II) (2.4 A). The active site contains a single Fe(II) ligated by three residues (His177, Asp179, and His234), and it is relatively open compared to those of the 2-oxoglutarate oxygenases. The side chains of Arg175 and Arg244, proposed to be involved in binding bicarbonate, project away from the active site, but conformational changes may allow either or both to enter the active site. The structures will form a basis for future mechanistic and inhibition studies.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Views of the Crystal Structure of ACCO Showing the Tetrameric and Dimeric Forms(A) shows tetrameric and (B) dimeric. The double-stranded helix (DSBH) cores are colored in red, non-core strands are colored in gold, and the helices are colored in green or blue for alternating monomers. Active site residues are drawn in ball and stick form. Individual ACCO monomers are assigned as m1, m2, m3 and m4.
Figure 3.
Figure 3. Overall View of the ACCO Structure and Comparison with ANS and IPNS(A) Stereoview of ACCO showing the double-stranded β-helix (DSBH) topology and the location of Fe(II) (in magenta). The α helices are in green, the DSBH core strands are in red, and non-core β strands are in gold. The side chains of Fe(II) binding residues (His177, Asp179, His234) and the ligating phosphate or sulfate are in ball and stick form. The extended helix α-3 is arrowed.(B) View of the structure of ANS (PDB 1GP5) complexed with Fe(II), 2OG, and dihydroquercetin. Two loops that help to enclose the ANS active site, making it more enclosed than that of ACCO in the crystalline form, are labeled as loops 1 and 2. The substrate and residues binding to Fe(II) atom are in ball and stick form. The color assignments for α helices and β strands are as in (A).(C) View from the crystal structure of the IPNS-Fe(II)-ACV (PDB 1BK0) complex showing the loop (labeled) and the C terminus that forms a “lid” over the active site. All color assignments are as in (A). Note that the ACCO active site is the most open, at least in the crystalline form (see text).
 
  The above figures are reprinted by permission from Cell Press: Chem Biol (2004, 11, 1383-1394) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21209891 F.Dahmani-Mardas, C.Troadec, A.Boualem, S.Lévêque, A.A.Alsadon, A.A.Aldoss, C.Dogimont, and A.Bendahmane (2010).
Engineering melon plants with improved fruit shelf life using the TILLING approach.
  PLoS One, 5, e15776.  
20830340 G.Baráth, J.Kaizer, J.S.Pap, G.Speier, N.El Bakkali-Taheri, and A.J.Simaan (2010).
Bio-inspired amino acid oxidation by a non-heme iron catalyst modeling the action of 1-aminocyclopropane-1-carboxylic acid oxidase.
  Chem Commun (Camb), 46, 7391-7393.  
19947658 M.A.Culpepper, E.E.Scott, and J.Limburg (2010).
Crystal structure of prolyl 4-hydroxylase from Bacillus anthracis.
  Biochemistry, 49, 124-133.
PDB code: 3itq
19567479 Z.Lin, S.Zhong, and D.Grierson (2009).
Recent advances in ethylene research.
  J Exp Bot, 60, 3311-3336.  
18238897 L.M.Mirica, and J.P.Klinman (2008).
The nature of O2 activation by the ethylene-forming enzyme 1-aminocyclopropane-1-carboxylic acid oxidase.
  Proc Natl Acad Sci U S A, 105, 1814-1819.  
19020684 P.C.Bruijnincx, G.van Koten, and R.J.Klein Gebbink (2008).
Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.
  Chem Soc Rev, 37, 2716-2744.  
18274607 W.Ghattas, M.Giorgi, C.Gaudin, A.Rockenbauer, M.Réglier, and A.J.Simaan (2007).
Characterization of Cu(II)-ACC complexes and conversion of the bound ACC into ethylene in the presence of hydrogen peroxide. detection of a brown intermediate at low temperature.
  Bioinorg Chem Appl, (), 43424.  
16705404 J.W.Hudgins, S.G.Ralph, V.R.Franceschi, and J.Bohlmann (2006).
Ethylene in induced conifer defense: cDNA cloning, protein expression, and cellular and subcellular localization of 1-aminocyclopropane-1-carboxylate oxidase in resin duct and phenolic parenchyma cells.
  Planta, 224, 865-877.  
16782814 M.A.McDonough, V.Li, E.Flashman, R.Chowdhury, C.Mohr, B.M.Liénard, J.Zondlo, N.J.Oldham, I.J.Clifton, J.Lewis, L.A.McNeill, R.J.Kurzeja, K.S.Hewitson, E.Yang, S.Jordan, R.S.Syed, and C.J.Schofield (2006).
Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2).
  Proc Natl Acad Sci U S A, 103, 9814-9819.
PDB codes: 2g19 2g1m
16491198 W.Ghattas, C.Gaudin, M.Giorgi, A.Rockenbauer, A.J.Simaan, and M.Réglier (2006).
ACC-Oxidase like activity of a copper (II)-ACC complex in the presence of hydrogen peroxide. Detection of a reaction intermediate at low temperature.
  Chem Commun (Camb), (), 1027-1029.  
16181493 D.R.Lester, A.Phillips, P.Hedden, and I.Andersson (2005).
Purification and kinetic studies of recombinant gibberellin dioxygenases.
  BMC Plant Biol, 5, 19.  
15739104 K.D.Koehntop, J.P.Emerson, and L.Que (2005).
The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes.
  J Biol Inorg Chem, 10, 87-93.  
16113715 N.J.Kershaw, M.E.Caines, M.C.Sleeman, and C.J.Schofield (2005).
The enzymology of clavam and carbapenem biosynthesis.
  Chem Commun (Camb), (), 4251-4263.  
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.