spacer
spacer

PDBsum entry 1pvd

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Lyase (carbon-carbon) PDB id
1pvd
Jmol
Contents
Protein chains
537 a.a. *
Ligands
TPP ×2
Metals
_MG ×2
Waters ×439
* Residue conservation analysis
PDB id:
1pvd
Name: Lyase (carbon-carbon)
Title: Crystal structure of the thiamin diphosphate dependent enzyme pyruvate decarboxylase from the yeast saccharomyces cerevisiae at 2.3 angstroms resolution
Structure: Pyruvate decarboxylase. Chain: a, b. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.165    
Authors: W.Furey,P.Arjunan
Key ref:
P.Arjunan et al. (1996). Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution. J Mol Biol, 256, 590-600. PubMed id: 8604141 DOI: 10.1006/jmbi.1996.0111
Date:
20-Apr-95     Release date:   31-Jul-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06169  (PDC1_YEAST) -  Pyruvate decarboxylase isozyme 1
Seq:
Struc:
 
Seq:
Struc:
563 a.a.
537 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     metabolic process   8 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
DOI no: 10.1006/jmbi.1996.0111 J Mol Biol 256:590-600 (1996)
PubMed id: 8604141  
 
 
Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution.
P.Arjunan, T.Umland, F.Dyda, S.Swaminathan, W.Furey, M.Sax, B.Farrenkopf, Y.Gao, D.Zhang, F.Jordan.
 
  ABSTRACT  
 
The crystal structure of pyruvate decarboxylase (EC 4.1.1.1), a thiamin diphosphate-dependent enzyme isolated from Saccharomyces cerevisiae, has been determined and refined to a resolution of 2.3 A. Pyruvate decarboxylase is a homotetrameric enzyme which crystallizes with two subunits in an asymmetric unit. The structure has been refined by a combination of simulated annealing and restrained least squares to an R factor of 0.165 for 46,787 reflections. As in the corresponding enzyme from Saccharomyces uvarum, the homotetrameric holoenzyme assembly has approximate 222 symmetry. In addition to providing more accurate atomic parameters and certainty in the sequence assignments, the high resolution and extensive refinement resulted in the identification of several tightly bound water molecules in key structural positions. These water molecules have low temperature factors and make several hydrogen bonds with protein residues. There are six such water molecules in each cofactor binding site, and one of them is involved in coordination with the required magnesium ion. Another may be involved in the catalytic reaction mechanism. The refined model includes 1074 amino acid residues (two subunits), two thiamin diphosphate cofactors, two magnesium ions associated with cofactor binding and 440 water molecules. From the refined model we conclude that the resting state of the enzyme-cofactor complex is such that the cofactor is already deprotonated at the N4' position of the pyrimidine ring, and is poised to accept a proton from the C2 position of the thiazolium ring.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Ribbon diagram for the PDC tetramer looking down the crystallographic 2-fold axis, generated by MOLSCRIPT (Kraulis, 1991). The ThDP cofactors are shown by a space-filling representation.
Figure 7.
Figure 7. The dimer interface environment around the catalytic center. The ThDP cofactor is situated at the interface between a and g domains from different subunits. Residues numbered <180 are from the a-domain and residues num- bered >360 are from the g-domain. Six water molecules (w1 to w6) are involved in hydrogen bonding with cofactor as well as with protein residues.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 256, 590-600) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20975902 A.Shrestha, S.Dhamwichukorn, and E.Jenwitheesuk (2010).
Modeling of pyruvate decarboxylases from ethanol producing bacteria.
  Bioinformation, 4, 378-384.  
20715795 D.Meyer, P.Neumann, C.Parthier, R.Friedemann, N.Nemeria, F.Jordan, and K.Tittmann (2010).
Double duty for a conserved glutamate in pyruvate decarboxylase: evidence of the participation in stereoelectronically controlled decarboxylation and in protonation of the nascent carbanion/enamine intermediate .
  Biochemistry, 49, 8197-8212.
PDB code: 3oe1
20099870 X.Y.Pei, K.M.Erixon, B.F.Luisi, and F.J.Leeper (2010).
Structural insights into the prereaction state of pyruvate decarboxylase from Zymomonas mobilis .
  Biochemistry, 49, 1727-1736.
PDB codes: 2wva 2wvg 2wvh
19490096 M.Müller, D.Gocke, and M.Pohl (2009).
Thiamin diphosphate in biological chemistry: exploitation of diverse thiamin diphosphate-dependent enzymes for asymmetric chemoenzymatic synthesis.
  FEBS J, 276, 2894-2904.  
19476485 N.S.Nemeria, S.Chakraborty, A.Balakrishnan, and F.Jordan (2009).
Reaction mechanisms of thiamin diphosphate enzymes: defining states of ionization and tautomerization of the cofactor at individual steps.
  FEBS J, 276, 2432-3446.  
19246454 S.Kutter, M.S.Weiss, G.Wille, R.Golbik, M.Spinka, and S.König (2009).
Covalently bound substrate at the regulatory site of yeast pyruvate decarboxylases triggers allosteric enzyme activation.
  J Biol Chem, 284, 12136-12144.
PDB codes: 2vjy 2vk1 2vk8
19630972 T.Soule, K.Palmer, Q.Gao, R.M.Potrafka, V.Stout, and F.Garcia-Pichel (2009).
A comparative genomics approach to understanding the biosynthesis of the sunscreen scytonemin in cyanobacteria.
  BMC Genomics, 10, 336.  
18224647 D.Gocke, L.Walter, E.Gauchenova, G.Kolter, M.Knoll, C.L.Berthold, G.Schneider, J.Pleiss, M.Müller, and M.Pohl (2008).
Rational protein design of ThDP-dependent enzymes-engineering stereoselectivity.
  Chembiochem, 9, 406-412.
PDB code: 2v3w
18058864 M.Alstrup Lie, and B.Schiøtt (2008).
A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models.
  J Comput Chem, 29, 1037-1047.  
18086676 T.Werther, M.Spinka, K.Tittmann, A.Schütz, R.Golbik, C.Mrestani-Klaus, G.Hübner, and S.König (2008).
Amino acids allosterically regulate the thiamine diphosphate-dependent alpha-keto acid decarboxylase from Mycobacterium tuberculosis.
  J Biol Chem, 283, 5344-5354.  
17182735 N.Nemeria, S.Chakraborty, A.Baykal, L.G.Korotchkina, M.S.Patel, and F.Jordan (2007).
The 1',4'-iminopyrimidine tautomer of thiamin diphosphate is poised for catalysis in asymmetric active centers on enzymes.
  Proc Natl Acad Sci U S A, 104, 78-82.  
17766418 S.Spaepen, W.Versées, D.Gocke, M.Pohl, J.Steyaert, and J.Vanderleyden (2007).
Characterization of phenylpyruvate decarboxylase, involved in auxin production of Azospirillum brasilense.
  J Bacteriol, 189, 7626-7633.  
17403037 W.Versées, S.Spaepen, J.Vanderleyden, and J.Steyaert (2007).
The crystal structure of phenylpyruvate decarboxylase from Azospirillum brasilense at 1.5 A resolution. Implications for its catalytic and regulatory mechanism.
  FEBS J, 274, 2363-2375.
PDB code: 2nxw
16768448 A.T.Baykal, L.Kakalis, and F.Jordan (2006).
Electronic and nuclear magnetic resonance spectroscopic features of the 1',4'-iminopyrimidine tautomeric form of thiamin diphosphate, a novel intermediate on enzymes requiring this coenzyme.
  Biochemistry, 45, 7522-7528.  
16862269 G.Malandrinos, M.Louloudi, and N.Hadjiliadis (2006).
Thiamine models and perspectives on the mechanism of action of thiamine-dependent enzymes.
  Chem Soc Rev, 35, 684-692.  
16680160 G.Wille, D.Meyer, A.Steinmetz, E.Hinze, R.Golbik, and K.Tittmann (2006).
The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.
  Nat Chem Biol, 2, 324-328.
PDB codes: 2ez4 2ez8 2ez9 2ezt 2ezu
16871614 J.Noeske, C.Richter, E.Stirnal, H.Schwalbe, and J.Wöhnert (2006).
Phosphate-group recognition by the aptamer domain of the thiamine pyrophosphate sensing riboswitch.
  Chembiochem, 7, 1451-1456.  
16531404 P.Arjunan, M.Sax, A.Brunskill, K.Chandrasekhar, N.Nemeria, S.Zhang, F.Jordan, and W.Furey (2006).
A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.
  J Biol Chem, 281, 15296-15303.
PDB codes: 2g25 2g28
16125473 P.Bell, K.Hoyt, and M.Shabangi (2006).
The electrochemical investigation of the catalytic power of pyruvate decarboxylase and its coenzyme.
  Bioelectrochemistry, 68, 171-174.  
16939618 S.Kutter, G.Wille, S.Relle, M.S.Weiss, G.Hübner, and S.König (2006).
The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis. Implications for the substrate activation mechanism of this enzyme.
  FEBS J, 273, 4199-4209.
PDB code: 2g1i
16216870 C.L.Berthold, P.Moussatche, N.G.Richards, and Y.Lindqvist (2005).
Structural basis for activation of the thiamin diphosphate-dependent enzyme oxalyl-CoA decarboxylase by adenosine diphosphate.
  J Biol Chem, 280, 41645-41654.
PDB code: 2c31
15923225 M.V.Petoukhov, and D.I.Svergun (2005).
Global rigid body modeling of macromolecular complexes against small-angle scattering data.
  Biophys J, 89, 1237-1250.  
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.  
15752351 R.Golbik, L.E.Meshalkina, T.Sandalova, K.Tittmann, E.Fiedler, H.Neef, S.König, R.Kluger, G.A.Kochetov, G.Schneider, and G.Hübner (2005).
Effect of coenzyme modification on the structural and catalytic properties of wild-type transketolase and of the variant E418A from Saccharomyces cerevisiae.
  FEBS J, 272, 1326-1342.  
15685598 S.Engel, M.Vyazmensky, D.Berkovich, Z.Barak, J.Merchuk, and D.M.Chipman (2005).
Column flow reactor using acetohydroxyacid synthase I from Escherichia coli as catalyst in continuous synthesis of R-phenylacetyl carbinol.
  Biotechnol Bioeng, 89, 733-740.  
16302970 T.G.Mosbacher, M.Mueller, and G.E.Schulz (2005).
Structure and mechanism of the ThDP-dependent benzaldehyde lyase from Pseudomonas fluorescens.
  FEBS J, 272, 6067-6076.
PDB codes: 2ag0 2ag1
15514144 F.Jordan (2004).
Biochemistry. How active sites communicate in thiamine enzymes.
  Science, 306, 818-820.  
14623876 M.E.Caines, J.M.Elkins, K.S.Hewitson, and C.J.Schofield (2004).
Crystal structure and mechanistic implications of N2-(2-carboxyethyl)arginine synthase, the first enzyme in the clavulanic acid biosynthesis pathway.
  J Biol Chem, 279, 5685-5692.
PDB codes: 1upa 1upb 1upc
15044456 S.Engel, M.Vyazmensky, M.Vinogradov, D.Berkovich, A.Bar-Ilan, U.Qimron, Y.Rosiansky, Z.Barak, and D.M.Chipman (2004).
Role of a conserved arginine in the mechanism of acetohydroxyacid synthase: catalysis of condensation with a specific ketoacid substrate.
  J Biol Chem, 279, 24803-24812.  
14557277 S.S.Pang, R.G.Duggleby, R.L.Schowen, and L.W.Guddat (2004).
The crystal structures of Klebsiella pneumoniae acetolactate synthase with enzyme-bound cofactor and with an unusual intermediate.
  J Biol Chem, 279, 2242-2253.
PDB codes: 1n0h 1ozf 1ozg 1ozh
12752452 A.Schütz, R.Golbik, K.Tittmann, D.I.Svergun, M.H.Koch, G.Hübner, and S.König (2003).
Studies on structure-function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway.
  Eur J Biochem, 270, 2322-2331.  
12752451 A.Schütz, T.Sandalova, S.Ricagno, G.Hübner, S.König, and G.Schneider (2003).
Crystal structure of thiamindiphosphate-dependent indolepyruvate decarboxylase from Enterobacter cloacae, an enzyme involved in the biosynthesis of the plant hormone indole-3-acetic acid.
  Eur J Biochem, 270, 2312-2321.
PDB code: 1ovm
12904299 G.Zhang, J.Dai, Z.Lu, and D.Dunaway-Mariano (2003).
The phosphonopyruvate decarboxylase from Bacteroides fragilis.
  J Biol Chem, 278, 41302-41308.  
14621995 M.Bhasin, J.L.Billinsky, and D.R.Palmer (2003).
Steady-state kinetics and molecular evolution of Escherichia coli MenD [(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], an anomalous thiamin diphosphate-dependent decarboxylase-carboligase.
  Biochemistry, 42, 13496-13504.  
11900538 E.A.Sergienko, and F.Jordan (2002).
New model for activation of yeast pyruvate decarboxylase by substrate consistent with the alternating sites mechanism: demonstration of the existence of two active forms of the enzyme.
  Biochemistry, 41, 3952-3967.  
11371467 D.I.Svergun, M.V.Petoukhov, and M.H.Koch (2001).
Determination of domain structure of proteins from X-ray solution scattering.
  Biophys J, 80, 2946-2953.  
11327837 J.Wang, R.Golbik, B.Seliger, M.Spinka, K.Tittmann, G.Hübner, and F.Jordan (2001).
Consequences of a modified putative substrate-activation site on catalysis by yeast pyruvate decarboxylase.
  Biochemistry, 40, 1755-1763.  
11435118 L.J.Baker, J.A.Dorocke, R.A.Harris, and D.E.Timm (2001).
The crystal structure of yeast thiamin pyrophosphokinase.
  Structure, 9, 539-546.
PDB code: 1ig0
11248689 M.Killenberg-Jabs, A.Jabs, H.Lilie, R.Golbik, and G.Hübner (2001).
Active oligomeric states of pyruvate decarboxylase and their functional characterization.
  Eur J Biochem, 268, 1698-1704.  
11526332 S.S.Pang, L.W.Guddat, and R.G.Duggleby (2001).
Crystallization of the catalytic subunit of Saccharomyces cerevisiae acetohydroxyacid synthase.
  Acta Crystallogr D Biol Crystallogr, 57, 1321-1323.  
10924138 A.K.Chang, P.F.Nixon, and R.G.Duggleby (2000).
Effects of deletions at the carboxyl terminus of Zymomonas mobilis pyruvate decarboxylase on the kinetic properties and substrate specificity.
  Biochemistry, 39, 9430-9437.  
10617618 D.I.Svergun, M.V.Petoukhov, M.H.Koch, and S.König (2000).
Crystal versus solution structures of thiamine diphosphate-dependent enzymes.
  J Biol Chem, 275, 297-302.  
11076527 E.A.Sergienko, J.Wang, L.Polovnikova, M.S.Hasson, M.J.McLeish, G.L.Kenyon, and F.Jordan (2000).
Spectroscopic detection of transient thiamin diphosphate-bound intermediates on benzoylformate decarboxylase.
  Biochemistry, 39, 13862-13869.  
10651824 G.Lu, D.Dobritzsch, S.Baumann, G.Schneider, and S.König (2000).
The structural basis of substrate activation in yeast pyruvate decarboxylase. A crystallographic and kinetic study.
  Eur J Biochem, 267, 861-868.
PDB code: 1qpb
11102784 O.P.Ward, and A.Singh (2000).
Enzymatic asymmetric synthesis by decarboxylases.
  Curr Opin Biotechnol, 11, 520-526.  
11029594 Y.G.Wu, A.K.Chang, P.F.Nixon, W.Li, and R.G.Duggleby (2000).
Mutagenesis at asp27 of pyruvate decarboxylase from Zymomonas mobilis. Effect on its ability to form acetoin and acetolactate.
  Eur J Biochem, 267, 6493-6500.  
10350453 F.Jordan, H.Li, and A.Brown (1999).
Remarkable stabilization of zwitterionic intermediates may account for a billion-fold rate acceleration by thiamin diphosphate-dependent decarboxylases.
  Biochemistry, 38, 6369-6373.  
10350464 H.J.Chiu, J.J.Reddick, T.P.Begley, and S.E.Ealick (1999).
Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 A resolution.
  Biochemistry, 38, 6460-6470.
PDB code: 2tps
10231381 I.Eberhardt, H.Cederberg, H.Li, S.König, F.Jordan, and S.Hohmann (1999).
Autoregulation of yeast pyruvate decarboxylase gene expression requires the enzyme but not its catalytic activity.
  Eur J Biochem, 262, 191-201.  
9765214 A.Warshel (1998).
Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites.
  J Biol Chem, 273, 27035-27038.  
9600897 A.Warshel, and J.Florián (1998).
Computer simulations of enzyme catalysis: finding out what has been optimized by evolution.
  Proc Natl Acad Sci U S A, 95, 5950-5955.  
9748345 F.Guo, D.Zhang, A.Kahyaoglu, R.S.Farid, and F.Jordan (1998).
Is a hydrophobic amino acid required to maintain the reactive V conformation of thiamin at the active center of thiamin diphosphate-requiring enzymes? Experimental and computational studies of isoleucine 415 of yeast pyruvate decarboxylase.
  Biochemistry, 37, 13379-13391.  
9655921 F.Jordan, N.Nemeria, F.Guo, I.Baburina, Y.Gao, A.Kahyaoglu, H.Li, J.Wang, J.Yi, J.R.Guest, and W.Furey (1998).
Regulation of thiamin diphosphate-dependent 2-oxo acid decarboxylases by substrate and thiamin diphosphate.Mg(II) - evidence for tertiary and quaternary interactions.
  Biochim Biophys Acta, 1385, 287-306.  
9924800 G.Schenk, R.G.Duggleby, and P.F.Nixon (1998).
Properties and functions of the thiamin diphosphate dependent enzyme transketolase.
  Int J Biochem Cell Biol, 30, 1297-1318.  
9655943 G.Schneider, and Y.Lindqvist (1998).
Crystallography and mutagenesis of transketolase: mechanistic implications for enzymatic thiamin catalysis.
  Biochim Biophys Acta, 1385, 387-398.  
9477950 I.Baburina, G.Dikdan, F.Guo, G.I.Tous, B.Root, and F.Jordan (1998).
Reactivity at the substrate activation site of yeast pyruvate decarboxylase: inhibition by distortion of domain interactions.
  Biochemistry, 37, 1245-1255.  
9477949 I.Baburina, H.Li, B.Bennion, W.Furey, and F.Jordan (1998).
Interdomain information transfer during substrate activation of yeast pyruvate decarboxylase: the interaction between cysteine 221 and histidine 92.
  Biochemistry, 37, 1235-1244.  
9655907 J.Hong, S.Sun, T.Derrick, C.Larive, K.B.Schowen, and R.L.Schowen (1998).
Transition-state theoretical interpretation of the catalytic power of pyruvate decarboxylases: the roles of static and dynamical considerations.
  Biochim Biophys Acta, 1385, 187-200.  
9655927 J.M.Candy, and R.G.Duggleby (1998).
Structure and properties of pyruvate decarboxylase and site-directed mutagenesis of the Zymomonas mobilis enzyme.
  Biochim Biophys Acta, 1385, 323-338.  
9665697 M.S.Hasson, A.Muscate, M.J.McLeish, L.S.Polovnikova, J.A.Gerlt, G.L.Kenyon, G.A.Petsko, and D.Ringe (1998).
The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
  Biochemistry, 37, 9918-9930.
PDB code: 1bfd
  9435065 P.Lu, B.P.Davis, and T.W.Jeffries (1998).
Cloning and characterization of two pyruvate decarboxylase genes from Pichia stipitis CBS 6054.
  Appl Environ Microbiol, 64, 94-97.  
9548765 S.König, D.I.Svergun, V.V.Volkov, L.A.Feigin, and M.H.Koch (1998).
Small-angle X-ray solution-scattering studies on ligand-induced subunit interactions of the thiamine diphosphate dependent enzyme pyruvate decarboxylase from different organisms.
  Biochemistry, 37, 5329-5334.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9310361 G.Schenk, F.J.Leeper, R.England, P.F.Nixon, and R.G.Duggleby (1997).
The role of His113 and His114 in pyruvate decarboxylase from Zymomonas mobilis.
  Eur J Biochem, 248, 63-71.  
9275170 K.Ma, A.Hutchins, S.J.Sung, and M.W.Adams (1997).
Pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon, Pyrococcus furiosus, functions as a CoA-dependent pyruvate decarboxylase.
  Proc Natl Acad Sci U S A, 94, 9608-9613.  
9048576 M.Killenberg-Jabs, S.König, I.Eberhardt, S.Hohmann, and G.Hübner (1997).
Role of Glu51 for cofactor binding and catalytic activity in pyruvate decarboxylase from yeast studied by site-directed mutagenesis.
  Biochemistry, 36, 1900-1905.  
9381974 R.A.Harris, J.W.Hawes, K.M.Popov, Y.Zhao, Y.Shimomura, J.Sato, J.Jaskiewicz, and T.D.Hurley (1997).
Studies on the regulation of the mitochondrial alpha-ketoacid dehydrogenase complexes and their kinases.
  Adv Enzyme Regul, 37, 271-293.  
8961951 C.K.Singleton, J.J.Wang, L.Shan, and P.R.Martin (1996).
Conserved residues are functionally distinct within transketolases of different species.
  Biochemistry, 35, 15865-15869.  
8973202 M.Ibdah, A.Bar-Ilan, O.Livnah, J.V.Schloss, Z.Barak, and D.M.Chipman (1996).
Homology modeling of the structure of bacterial acetohydroxy acid synthase and examination of the active site by site-directed mutagenesis.
  Biochemistry, 35, 16282-16291.  
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.