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PDBsum entry 2sqc

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
2sqc
Jmol
Contents
Protein chains
623 a.a. *
Ligands
C8E ×6
Waters ×1515
* Residue conservation analysis
PDB id:
2sqc
Name: Isomerase
Title: Squalene-hopene cyclase from alicyclobacillus acidocaldarius
Structure: Squalene-hopene cyclase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Alicyclobacillus acidocaldarius. Organism_taxid: 405212. Cell_line: jm105. Atcc: atcc 27009. Collection: atcc 27009. Cellular_location: membrane. Expressed in: escherichia coli k12. Expression_system_taxid: 83333. Expression_system_cell_line: jm105.
Resolution:
2.00Å     R-factor:   0.153     R-free:   0.187
Authors: K.U.Wendt,G.E.Schulz
Key ref:
K.U.Wendt et al. (1999). The structure of the membrane protein squalene-hopene cyclase at 2.0 A resolution. J Mol Biol, 286, 175-187. PubMed id: 9931258 DOI: 10.1006/jmbi.1998.2470
Date:
02-Aug-98     Release date:   27-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P33247  (SQHC_ALIAD) -  Squalene--hopene cyclase
Seq:
Struc:
 
Seq:
Struc:
631 a.a.
623 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: E.C.4.2.1.129  - Squalene--hopanol cyclase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hopan-22-ol = squalene + H2O
Hopan-22-ol
= squalene
+ H(2)O
   Enzyme class 3: E.C.5.4.99.17  - Squalene--hopene cyclase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: Squalene = hop-2229-ene
Squalene
= hop-22(29)-ene
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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     hopanoid biosynthetic process   1 term 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1998.2470 J Mol Biol 286:175-187 (1999)
PubMed id: 9931258  
 
 
The structure of the membrane protein squalene-hopene cyclase at 2.0 A resolution.
K.U.Wendt, A.Lenhart, G.E.Schulz.
 
  ABSTRACT  
 
Squalene cyclases catalyze a cationic cyclization cascade, which is homologous to a key step in cholesterol biosynthesis. The structure of the enzyme from Alicyclobacillus acidocaldarius has been determined in a new crystal form at 2.0 A resolution (1 A=0.1 nm) and refined to an R-factor of 15.3 % (Rfree=18.7 %). The structure indicates how the initial protonation and the final deprotonation of squalene occur and how the transient carbocations are stabilized. The pathways of the flexible educt squalene from the membrane interior to the active center cavity and of the rigid fused-ring product hopene in the reverse direction are discussed. The enzyme contains eight so-called QW-sequence repeats that fortify the alpha/alpha-barrels by an intricate interaction network. They are unique to the known triterpene cyclases and are presumed to shield these enzymes against the released enthalpy of the highly exergonic catalyzed reaction. The enzyme is a monotopic membrane protein, the membrane-binding interactions of which are described and compared with those of two prostaglandin-H2 synthase isoenzymes, the only other structurally characterized proteins of this type. In the crystals the membrane-binding regions face each other, suggesting a micelle-type detergent structure between them.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Surface representations [Nicholls et al 1991] of the two structurally known monotopic membrane proteins color-coded for non-polar (yellow), positive (blue) and negative (red) areas. (a) Proposed model for SHC-binding to the membrane. The two non-polar plateaux are oriented in parallel and reach with their channel entrances E into the non-polar part of the membrane where squalene is dissolved. The non-polar pocket binding a C[8]E[4] molecule at the interface is marked by an x. (b) View from the membrane onto the two non-polar plateaux of the SHC dimer. Four ligated C[8]E[4] detergent molecules are included. (c) View from the membrane onto dimeric prostaglandin-H[2] synthase-I with the ligated detergent b-octylglucoside [Loll et al 1995]. The arrows indicate the presumed passage for the polar headgroup of the substrate arachidonic acid from the lipid bilayer to the entrance of the active center pocket.
Figure 11.
Figure 11. Stereo view of the structure consisting of QW-repeat r6 together with the front region of r7. Two outer (red) and one inner (yellow) barrel-helices are depicted with one core region (green, residues drawn out to the C^b atom). Hydrogen bonds are represented by dots. For the core regions, the average deviation of all pairwise comparisons except r4 is 0.23 Å, which is around the error limit. The core of r4 forms a long loop that returns to the tryptophan position, which however, carries a phenylalanine (Figure 10).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 286, 175-187) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21315729 G.E.Schulz (2011).
A new classification of membrane protein crystals.
  J Mol Biol, 407, 640-646.  
20304090 P.D.Kiser, and K.Palczewski (2010).
Membrane-binding and enzymatic properties of RPE65.
  Prog Retin Eye Res, 29, 428-442.  
19897737 T.M.Joffrion, M.S.Collins, T.Sesterhenn, and M.T.Cushion (2010).
Functional characterization and localization of Pneumocystis carinii lanosterol synthase.
  Eukaryot Cell, 9, 107-115.  
19487671 M.Marcia, U.Ermler, G.Peng, and H.Michel (2009).
The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration.
  Proc Natl Acad Sci U S A, 106, 9625-9630.
PDB codes: 3h27 3h28 3h29 3hyv 3hyw 3hyx
19207562 T.Frickey, and E.Kannenberg (2009).
Phylogenetic analysis of the triterpene cyclase protein family in prokaryotes and eukaryotes suggests bidirectional lateral gene transfer.
  Environ Microbiol, 11, 1224-1241.  
18033581 I.Abe (2007).
Enzymatic synthesis of cyclic triterpenes.
  Nat Prod Rep, 24, 1311-1331.  
17482885 U.C.Tran, and C.F.Clarke (2007).
Endogenous synthesis of coenzyme Q in eukaryotes.
  Mitochondrion, 7, S62-S71.  
17046834 H.R.Corradi, A.V.Corrigall, E.Boix, C.G.Mohan, E.D.Sturrock, P.N.Meissner, and K.R.Acharya (2006).
Crystal structure of protoporphyrinogen oxidase from Myxococcus xanthus and its complex with the inhibitor acifluorfen.
  J Biol Chem, 281, 38625-38633.
PDB codes: 2ivd 2ive
17050691 J.Zhang, F.E.Frerman, and J.J.Kim (2006).
Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
  Proc Natl Acad Sci U S A, 103, 16212-16217.
PDB codes: 2gmh 2gmj
17030994 S.D.Gilk, Y.Raviv, K.Hu, J.M.Murray, C.J.Beckers, and G.E.Ward (2006).
Identification of PhIL1, a novel cytoskeletal protein of the Toxoplasma gondii pellicle, through photosensitized labeling with 5-[125I]iodonaphthalene-1-azide.
  Eukaryot Cell, 5, 1622-1634.  
16446812 S.P.Matsuda, W.K.Wilson, and Q.Xiong (2006).
Mechanistic insights into triterpene synthesis from quantum mechanical calculations. Detection of systematic errors in B3LYP cyclization energies.
  Org Biomol Chem, 4, 530-543.  
16140766 C.Fetzer, B.A.Tews, and G.Meyers (2005).
The carboxy-terminal sequence of the pestivirus glycoprotein E(rns) represents an unusual type of membrane anchor.
  J Virol, 79, 11901-11913.  
15821095 D.P.Kloer, S.Ruch, S.Al-Babili, P.Beyer, and G.E.Schulz (2005).
The structure of a retinal-forming carotenoid oxygenase.
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PDB codes: 2biw 2bix
16289312 F.Bouvier, A.Rahier, and B.Camara (2005).
Biogenesis, molecular regulation and function of plant isoprenoids.
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15929157 K.U.Wendt (2005).
Enzyme mechanisms for triterpene cyclization: new pieces of the puzzle.
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  Mol Divers, 9, 171-186.  
16351060 R.A.Yoder, and J.N.Johnston (2005).
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  Chem Rev, 105, 4730-4756.  
16235265 S.Oliaro-Bosso, T.Schulz-Gasch, G.Balliano, and F.Viola (2005).
Access of the substrate to the active site of yeast oxidosqualene cyclase: an inhibition and site-directed mutagenesis approach.
  Chembiochem, 6, 2221-2228.  
16106294 T.Abe, and T.Hoshino (2005).
Enzymatic cyclizations of squalene analogs with threo- and erythro-diols at the 6,7- or 10,11-positions by recombinant squalene cyclase. Trapping of carbocation intermediates and mechanistic insights into the product and substrate specificities.
  Org Biomol Chem, 3, 3127-3139.  
15113001 D.J.Reinert, G.Balliano, and G.E.Schulz (2004).
Conversion of squalene to the pentacarbocyclic hopene.
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PDB code: 1ump
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PDB codes: 1r7c 1r7d 1r7e 1r7f 1r7g
15467228 G.Cravotto, G.Balliano, S.Tagliapietra, S.Oliaro-Bosso, and G.M.Nano (2004).
Novel squalene-hopene cyclase inhibitors derived from hydroxycoumarins and hydroxyacetophenones.
  Chem Pharm Bull (Tokyo), 52, 1171-1174.  
15112988 K.Poralla (2004).
Profound insights into squalene cyclization.
  Chem Biol, 11, 12-14.  
15057273 M.Koch, C.Breithaupt, R.Kiefersauer, J.Freigang, R.Huber, and A.Messerschmidt (2004).
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PDB code: 1sez
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Insight into steroid scaffold formation from the structure of human oxidosqualene cyclase.
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PDB codes: 1w6j 1w6k
15515077 S.Lodeiro, M.J.Segura, M.Stahl, T.Schulz-Gasch, and S.P.Matsuda (2004).
Oxidosqualene cyclase second-sphere residues profoundly influence the product profile.
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15691023 S.Oliaro-Bosso, F.Viola, S.Matsuda, G.Cravotto, S.Tagliapietra, and G.Balliano (2004).
Umbelliferone aminoalkyl derivatives as inhibitors of oxidosqualene cyclases from Saccharomyces cerevisiae, Trypanosoma cruzi, and Pneumocystis carinii.
  Lipids, 39, 1007-1012.  
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  Angew Chem Int Ed Engl, 43, 6700-6703.  
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Site-directed mutagenesis experiments on the putative deprotonation site of squalene-hopene cyclase from Alicyclobacillus acidocaldarius.
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12784859 F.Rocco, S.O.Bosso, F.Viola, P.Milla, G.Roma, G.Grossi, and M.Ceruti (2003).
Conjugated methyl sulfide and phenyl sulfide derivatives of oxidosqualene as inhibitors of oxidosqualene and squalene-hopene cyclases.
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14529268 N.Miled, A.Roussel, C.Bussetta, L.Berti-Dupuis, M.Rivière, G.Buono, R.Verger, C.Cambillau, and S.Canaan (2003).
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Protein prenyltransferases.
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11911193 J.Binet, D.Thomas, A.Benmbarek, F.D.de, and P.Renaut (2002).
Structure activity relationships of new inhibitors of mammalian 2,3-oxidosqualene cyclase designed from isoquinoline derivatives.
  Chem Pharm Bull (Tokyo), 50, 316-329.  
11985588 P.Milla, A.Lenhart, G.Grosa, F.Viola, W.A.Weihofen, G.E.Schulz, and G.Balliano (2002).
Thiol-modifying inhibitors for understanding squalene cyclase function.
  Eur J Biochem, 269, 2108-2116.  
12617471 P.Milla, F.Viola, S.Oliaro Bosso, F.Rocco, L.Cattel, B.M.Joubert, R.J.LeClair, S.P.Matsuda, and G.Balliano (2002).
Subcellular localization of oxidosqualene cyclases from Arabidopsis thaliana, Trypanosoma cruzi, and Pneumocystis carinii expressed in yeast.
  Lipids, 37, 1171-1176.  
12081472 T.K.Wu, and J.H.Griffin (2002).
Conversion of a plant oxidosqualene-cycloartenol synthase to an oxidosqualene-lanosterol cyclase by random mutagenesis.
  Biochemistry, 41, 8238-8244.  
12353625 T.Sato, S.Sasahara, T.Yamakami, and T.Hoshino (2002).
Functional analyses of Tyr420 and Leu607 of Alicyclobacillus acidocaldarius squalene-hopene cyclase. Neoachillapentaene, a novel triterpene with the 1,5,6-trimethylcyclohexene moiety produced through folding of the constrained boat structure.
  Biosci Biotechnol Biochem, 66, 1660-1670.  
11231284 J.M.Bravo, M.Perzl, T.Härtner, E.L.Kannenberg, and M.Rohmer (2001).
Novel methylated triterpenoids of the gammacerane series from the nitrogen-fixing bacterium Bradyrhizobium japonicum USDA 110.
  Eur J Biochem, 268, 1323-1331.  
11758915 T.Sato, and T.Hoshino (2001).
Catalytic function of the residues of phenylalanine and tyrosine conserved in squalene-hopene cyclases.
  Biosci Biotechnol Biochem, 65, 2233-2242.  
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Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase.
  EMBO J, 20, 1530-1537.
PDB codes: 1hx3 1hzt
  10675587 C.Füll, and K.Poralla (2000).
Conserved tyr residues determine functions of Alicyclobacillus acidocaldarius squalene-hopene cyclase.
  FEMS Microbiol Lett, 183, 221-224.  
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New insight into the structure and function of the alternative oxidase.
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A class of 4-aza-lithocholic acid-derived haptens for the generation of catalytic antibodies with steroid synthase capabilities.
  Bioorg Med Chem, 8, 995.  
10966478 J.L.Popot, and D.M.Engelman (2000).
Helical membrane protein folding, stability, and evolution.
  Annu Rev Biochem, 69, 881-922.  
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Enzyme Mechanisms for Polycyclic Triterpene Formation.
  Angew Chem Int Ed Engl, 39, 2812-2833.  
11093215 M.M.Meyer, M.J.Segura, W.K.Wilson, and S.P.Matsuda (2000).
Oxidosqualene Cyclase Residues that Promote Formation of Cycloartenol, Lanosterol, and Parkeol We are grateful to Bridget M. Joubert for advice regarding mutagenesis. We thank Elizabeth A. Hart for an authentic parkeol standard, and for chromatographic and spectroscopic information. This research was funded by the National Institutes of Health (grant no. AI 41598) and the Robert A. Welch Foundation (grant no. C-1323). M.M.M. was an American Society of Pharmacognosy Undergraduate Fellow. M.J.R.S. was a Robert A. Welch Fellow and was supported by an NIH Biotechnology Training Grant (grant no. T32 GM08362).
  Angew Chem Int Ed Engl, 39, 4090-4092.  
10783001 S.M.Godzina, M.A.Lovato, M.M.Meyer, K.A.Foster, W.K.Wilson, W.Gu, E.L.de Hostos, and S.P.Matsuda (2000).
Cloning and characterization of the Dictyostelium discoideum cycloartenol synthase cDNA.
  Lipids, 35, 249-255.  
11027990 S.Z.Zhou, M.Sey, De Clercq PJ, M.Milanesio, and D.Viterbo (2000).
A Model for the Nonenzymatic BCD Cyclization of Squalene This research was supported by FWO-Vlaanderen. We thank Dr. Davide Proserpio (Università di Milano) and Dr. Annalisa Guerri (Università di Firenze) for the allowance to use the CCD diffractometers.
  Angew Chem Int Ed Engl, 39, 2861-2863.  
11048954 T.Dang, and G.D.Prestwich (2000).
Site-directed mutagenesis of squalene-hopene cyclase: altered substrate specificity and product distribution.
  Chem Biol, 7, 643-649.  
11111077 T.R.Tansey, and I.Shechter (2000).
Structure and regulation of mammalian squalene synthase.
  Biochim Biophys Acta, 1529, 49-62.  
10966456 W.L.Smith, D.L.DeWitt, and R.M.Garavito (2000).
Cyclooxygenases: structural, cellular, and molecular biology.
  Annu Rev Biochem, 69, 145-182.  
10551860 A.G.Spencer, E.Thuresson, J.C.Otto, I.Song, T.Smith, D.L.DeWitt, R.M.Garavito, and W.L.Smith (1999).
The membrane binding domains of prostaglandin endoperoxide H synthases 1 and 2. Peptide mapping and mutational analysis.
  J Biol Chem, 274, 32936-32942.  
10375539 T.Dang, I.Abe, Y.F.Zheng, and G.D.Prestwich (1999).
The binding site for an inhibitor of squalene:hopene cyclase determined using photoaffinity labeling and molecular modeling.
  Chem Biol, 6, 333-341.  
10635573 T.Hoshino, M.Kouda, T.Abe, and S.Ohashi (1999).
New cyclization mechanism for squalene: a ring-expansion step for the five-membered C-ring intermediate in hopene biosynthesis.
  Biosci Biotechnol Biochem, 63, 2038-2041.  
10664852 T.Sato, and T.Hoshino (1999).
Functional analysis of the DXDDTA motif in squalene-hopene cyclase by site-directed mutagenesis experiments: initiation site of the polycyclization reaction and stabilization site of the carbocation intermediate of the initially cyclized A-ring.
  Biosci Biotechnol Biochem, 63, 2189-2198.  
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.