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PDBsum entry 2tys

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
2tys
Jmol
Contents
Protein chains
255 a.a. *
395 a.a. *
Ligands
PLT
Metals
_NA
Waters ×358
* Residue conservation analysis
PDB id:
2tys
Name: Lyase
Title: Crystal structures of mutant (betak87t) tryptophan synthase alpha2 beta2 complex with ligands bound to the active sites of the alpha and beta subunits reveal ligand-induced conformational changes
Structure: Tryptophan synthase. Chain: a. Engineered: yes. Mutation: yes. Other_details: l-tryptophan bound to the beta subunit in a form of schiff base with coenzyme pyridoxal 5'-phosphate. Tryptophan synthase. Chain: b. Engineered: yes.
Source: Salmonella typhimurium. Organism_taxid: 602. Cell_line: cb149. Gene: trpa/trpb. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: cb149.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.90Å     R-factor:   0.171    
Authors: S.Rhee,K.D.Parris,C.C.Hyde,S.A.Ahmed,E.W.Miles,D.R.Davies
Key ref:
S.Rhee et al. (1997). Crystal structures of a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with ligands bound to the active sites of the alpha- and beta-subunits reveal ligand-induced conformational changes. Biochemistry, 36, 7664-7680. PubMed id: 9201907 DOI: 10.1021/bi9700429
Date:
08-Jan-97     Release date:   01-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00929  (TRPA_SALTY) -  Tryptophan synthase alpha chain
Seq:
Struc:
268 a.a.
255 a.a.
Protein chain
Pfam   ArchSchema ?
P0A2K1  (TRPB_SALTY) -  Tryptophan synthase beta chain
Seq:
Struc:
397 a.a.
395 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.4.2.1.20  - Tryptophan synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Tryptophan Biosynthesis
      Reaction: L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + D-glyceraldehyde 3-phosphate + H2O
L-serine
+ 1-C-(indol-3-yl)glycerol 3-phosphate
=
L-tryptophan
Bound ligand (Het Group name = PLT)
matches with 50.00% similarity
+ D-glyceraldehyde 3-phosphate
+ H(2)O
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi9700429 Biochemistry 36:7664-7680 (1997)
PubMed id: 9201907  
 
 
Crystal structures of a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with ligands bound to the active sites of the alpha- and beta-subunits reveal ligand-induced conformational changes.
S.Rhee, K.D.Parris, C.C.Hyde, S.A.Ahmed, E.W.Miles, D.R.Davies.
 
  ABSTRACT  
 
Three-dimensional structures are reported for a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with either the substrate L-serine (betaK87T-Ser) or product L-tryptophan (betaK87T-Trp) at the active site of the beta-subunit, in which both amino acids form external aldimines with the coenzyme, pyridoxal phosphate. We also present structures with L-serine bound to the beta site and either alpha-glycerol 3-phosphate (betaK87T-Ser-GP) or indole-3-propanol phosphate (betaK87T-Ser-IPP) bound to the active site of the alpha-subunit. The results further identify the substrate and product binding sites in each subunit and provide insight into conformational changes that occur upon formation of these complexes. The two structures having ligands at the active sites of both alpha- and beta-subunits reveal an important new feature, the ordering of alpha-subunit loop 6 (residues 179-187). Closure of loop 6 isolates the active site of the alpha-subunit from solvent and results in interaction between alphaThr183 and the catalytic residue alphaAsp60. Other conformational differences between the wild type and these two mutant structures include a rigid-body rotation of the alpha-subunit of approximately 5 degrees relative to the beta-subunit and large movements of part of the beta-subunit (residues 93-189) toward the rest of the beta-subunit. Much smaller differences are observed in the betaK87T-Ser structure. Remarkably, binding of tryptophan to the beta active site results in conformational changes very similar to those observed in the betaK87T-Ser-GP and betaK87T-Ser-IPP structures, with exception of the disordered alpha-subunit loop 6. These large-scale changes, the closure of loop 6, and the movements of a small number of side chains in the alpha-beta interaction site provide a structural base for interpreting the allosteric properties of tryptophan synthase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20370823 K.Nishio, K.Ogasahara, Y.Morimoto, T.Tsukihara, S.J.Lee, and K.Yutani (2010).
Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding.
  FEBS J, 277, 2157-2170.
PDB codes: 2dh5 2dh6
20233374 R.S.Phillips, E.W.Miles, P.McPhie, S.Marchal, R.Lange, G.Holtermann, and R.S.Goody (2010).
Effects of hydrostatic pressure on the conformational equilibrium of tryptophan synthase from Salmonella typhimurium.
  Ann N Y Acad Sci, 1189, 95.  
19430702 H.Shen, Y.Yang, F.Wang, Y.Zhang, N.Ye, S.Xu, and H.Wang (2009).
Characterization of the putative tryptophan synthase beta-subunit from Mycobacterium tuberculosis.
  Acta Biochim Biophys Sin (Shanghai), 41, 379-388.  
19640845 M.Goto, T.Yamauchi, N.Kamiya, I.Miyahara, T.Yoshimura, H.Mihara, T.Kurihara, K.Hirotsu, and N.Esaki (2009).
Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe.
  J Biol Chem, 284, 25944-25952.
PDB codes: 1wtc 2zr8
19387555 S.Raboni, S.Bettati, and A.Mozzarelli (2009).
Tryptophan synthase: a mine for enzymologists.
  Cell Mol Life Sci, 66, 2391-2403.  
18486479 M.F.Dunn, D.Niks, H.Ngo, T.R.Barends, and I.Schlichting (2008).
Tryptophan synthase: the workings of a channeling nanomachine.
  Trends Biochem Sci, 33, 254-264.  
17932934 S.Wong, and M.P.Jacobson (2008).
Conformational selection in silico: loop latching motions and ligand binding in enzymes.
  Proteins, 71, 153-164.  
18675375 T.R.Barends, M.F.Dunn, and I.Schlichting (2008).
Tryptophan synthase, an allosteric molecular factory.
  Curr Opin Chem Biol, 12, 593-600.  
18351684 T.R.Barends, T.Domratcheva, V.Kulik, L.Blumenstein, D.Niks, M.F.Dunn, and I.Schlichting (2008).
Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate.
  Chembiochem, 9, 1024-1028.
PDB code: 3cep
18757725 Y.Wu, E.Kondrashkina, C.Kayatekin, C.R.Matthews, and O.Bilsel (2008).
Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein.
  Proc Natl Acad Sci U S A, 105, 13367-13372.  
18063718 F.R.Tabita, T.E.Hanson, H.Li, S.Satagopan, J.Singh, and S.Chan (2007).
Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs.
  Microbiol Mol Biol Rev, 71, 576-599.
PDB code: 2qyg
15691828 S.Raboni, S.Bettati, and A.Mozzarelli (2005).
Identification of the geometric requirements for allosteric communication between the alpha- and beta-subunits of tryptophan synthase.
  J Biol Chem, 280, 13450-13456.  
15117965 F.Schiaretti, S.Bettati, C.Viappiani, and A.Mozzarelli (2004).
pH dependence of tryptophan synthase catalytic mechanism: I. The first stage, the beta-elimination reaction.
  J Biol Chem, 279, 29572-29582.  
15356864 G.André, and V.Tran (2004).
Putative implication of alpha-amylase loop 7 in the mechanism of substrate binding and reaction products release.
  Biopolymers, 75, 95.  
15206928 Y.Hioki, K.Ogasahara, S.J.Lee, J.Ma, M.Ishida, Y.Yamagata, Y.Matsuura, M.Ota, M.Ikeguchi, S.Kuramitsu, and K.Yutani (2004).
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.
  Eur J Biochem, 271, 2624-2635.
PDB code: 1v8z
12939261 A.Osborne, Q.Teng, E.W.Miles, and R.S.Phillips (2003).
Detection of open and closed conformations of tryptophan synthase by 15N-heteronuclear single-quantum coherence nuclear magnetic resonance of bound 1-15N-L-tryptophan.
  J Biol Chem, 278, 44083-44090.  
12643278 K.Ogasahara, M.Ishida, and K.Yutani (2003).
Stimulated interaction between and subunits of tryptophan synthase from hyperthermophile enhances its thermal stability.
  J Biol Chem, 278, 8922-8928.  
12952961 R.Omi, M.Goto, I.Miyahara, H.Mizuguchi, H.Hayashi, H.Kagamiyama, and K.Hirotsu (2003).
Crystal structures of threonine synthase from Thermus thermophilus HB8: conformational change, substrate recognition, and mechanism.
  J Biol Chem, 278, 46035-46045.
PDB codes: 1uim 1uin 1uiq 1v7c
12882962 T.Ose, A.Fujino, M.Yao, N.Watanabe, M.Honma, and I.Tanaka (2003).
Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction.
  J Biol Chem, 278, 41069-41076.
PDB codes: 1j0c 1j0d 1j0e
14596599 T.Yamada, J.Komoto, Y.Takata, H.Ogawa, H.C.Pitot, and F.Takusagawa (2003).
Crystal structure of serine dehydratase from rat liver.
  Biochemistry, 42, 12854-12865.
PDB codes: 1pwe 1pwh
  11806827 G.Xie, C.Forst, C.Bonner, and R.A.Jensen (2002).
Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants.
  Genome Biol, 3, RESEARCH0004.  
11756443 M.Garrido-Franco, S.Ehlert, A.Messerschmidt, S.Marinkovic', R.Huber, B.Laber, G.P.Bourenkov, and T.Clausen (2002).
Structure and function of threonine synthase from yeast.
  J Biol Chem, 277, 12396-12405.
PDB code: 1kl7
11756456 M.Weyand, I.Schlichting, A.Marabotti, and A.Mozzarelli (2002).
Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase.
  J Biol Chem, 277, 10647-10652.
PDB codes: 1k3u 1k7e 1k7f
11756454 M.Weyand, I.Schlichting, P.Herde, A.Marabotti, and A.Mozzarelli (2002).
Crystal structure of the beta Ser178--> Pro mutant of tryptophan synthase. A "knock-out" allosteric enzyme.
  J Biol Chem, 277, 10653-10660.
PDB codes: 1k7x 1k8y 1k8z
12146963 O.Hur, D.Niks, P.Casino, and M.F.Dunn (2002).
Proton transfers in the beta-reaction catalyzed by tryptophan synthase.
  Biochemistry, 41, 9991.  
12146962 R.M.Harris, and M.F.Dunn (2002).
Intermediate trapping via a conformational switch in the Na(+)-activated tryptophan synthase bienzyme complex.
  Biochemistry, 41, 9982-9990.  
11756459 S.Hettwer, and R.Sterner (2002).
A novel tryptophan synthase beta-subunit from the hyperthermophile Thermotoga maritima. Quaternary structure, steady-state kinetics, and putative physiological role.
  J Biol Chem, 277, 8194-8201.  
11893063 E.W.Miles (2001).
Tryptophan synthase: a multienzyme complex with an intramolecular tunnel.
  Chem Rec, 1, 140-151.  
11297416 E.Weber-Ban, O.Hur, C.Bagwell, U.Banik, L.H.Yang, E.W.Miles, and M.F.Dunn (2001).
Investigation of allosteric linkages in the regulation of tryptophan synthase: the roles of salt bridges and monovalent cations probed by site-directed mutation, optical spectroscopy, and kinetics.
  Biochemistry, 40, 3497-3511.  
11395405 X.Huang, H.M.Holden, and F.M.Raushel (2001).
Channeling of substrates and intermediates in enzyme-catalyzed reactions.
  Annu Rev Biochem, 70, 149-180.  
10702257 A.Mozzarelli, A.Peracchi, B.Rovegno, G.Dalè, G.L.Rossi, and M.F.Dunn (2000).
Effect of pH and monovalent cations on the formation of quinonoid intermediates of the tryptophan synthase alpha(2)beta(2) complex in solution and in the crystal.
  J Biol Chem, 275, 6956-6962.  
11009609 D.Liu, W.E.Karsten, and P.F.Cook (2000).
Lysine 199 is the general acid in the NAD-malic enzyme reaction.
  Biochemistry, 39, 11955-11960.  
10758003 F.M.McMillan, M.Cahoon, A.White, L.Hedstrom, G.A.Petsko, and D.Ringe (2000).
Crystal structure at 2.4 A resolution of Borrelia burgdorferi inosine 5'-monophosphate dehydrogenase: evidence of a substrate-induced hinged-lid motion by loop 6.
  Biochemistry, 39, 4533-4542.
PDB code: 1eep
10673430 G.Schneider, H.Käck, and Y.Lindqvist (2000).
The manifold of vitamin B6 dependent enzymes.
  Structure, 8, R1-R6.  
10692338 G.Zhou, W.R.Ellington, and M.S.Chapman (2000).
Induced fit in arginine kinase.
  Biophys J, 78, 1541-1550.  
11209753 P.Rondard, and H.Bedouelle (2000).
Mutational scanning of a hairpin loop in the tryptophan synthase beta-subunit implicated in allostery and substrate channeling.
  Biol Chem, 381, 1185-1193.  
10737185 Y.J.Jia, H.Ito, H.Matsui, and M.Honma (2000).
1-aminocyclopropane-1-carboxylate (ACC) deaminase induced by ACC synthesized and accumulated in Penicillium citrinum intracellular spaces.
  Biosci Biotechnol Biochem, 64, 299-305.  
10769125 Y.X.Fan, P.McPhie, and E.W.Miles (2000).
Regulation of tryptophan synthase by temperature, monovalent cations, and an allosteric ligand. Evidence from Arrhenius plots, absorption spectra, and primary kinetic isotope effects.
  Biochemistry, 39, 4692-4703.  
10079072 A.A.Morollo, G.A.Petsko, and D.Ringe (1999).
Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.
  Biochemistry, 38, 3293-3301.
PDB code: 2sfp
10212181 E.W.Miles, S.Rhee, and D.R.Davies (1999).
The molecular basis of substrate channeling.
  J Biol Chem, 274, 12193-12196.  
10353822 E.Woehl, and M.F.Dunn (1999).
Mechanisms of monovalent cation action in enzyme catalysis: the first stage of the tryptophan synthase beta-reaction.
  Biochemistry, 38, 7118-7130.  
10353823 E.Woehl, and M.F.Dunn (1999).
Mechanisms of monovalent cation action in enzyme catalysis: the tryptophan synthase alpha-, beta-, and alpha beta-reactions.
  Biochemistry, 38, 7131-7141.  
10593940 H.S.Ro, and E.W.Miles (1999).
Structure and function of the tryptophan synthase alpha(2)beta(2) complex. Roles of beta subunit histidine 86.
  J Biol Chem, 274, 36439-36445.  
10531312 H.S.Ro, and E.Wilson Miles (1999).
Catalytic mechanism of the tryptophan synthase alpha(2)beta(2) complex. Effects of pH, isotopic substitution, and allosteric ligands.
  J Biol Chem, 274, 31189-31194.  
10090734 I.Bahar, and R.L.Jernigan (1999).
Cooperative fluctuations and subunit communication in tryptophan synthase.
  Biochemistry, 38, 3478-3490.  
10601247 K.D.Schnackerz, C.H.Tai, R.K.Pötsch, and P.F.Cook (1999).
Substitution of pyridoxal 5'-phosphate in D-serine dehydratase from Escherichia coli by cofactor analogues provides information on cofactor binding and catalysis.
  J Biol Chem, 274, 36935-36943.  
10026165 M.Bertoldi, P.Frigeri, M.Paci, and C.B.Voltattorni (1999).
Reaction specificity of native and nicked 3,4-dihydroxyphenylalanine decarboxylase.
  J Biol Chem, 274, 5514-5521.  
10600108 M.Weyand, and I.Schlichting (1999).
Crystal structure of wild-type tryptophan synthase complexed with the natural substrate indole-3-glycerol phosphate.
  Biochemistry, 38, 16469-16480.
PDB codes: 1qop 1qoq
10449718 T.Knöchel, A.Ivens, G.Hester, A.Gonzalez, R.Bauerle, M.Wilmanns, K.Kirschner, and J.N.Jansonius (1999).
The crystal structure of anthranilate synthase from Sulfolobus solfataricus: functional implications.
  Proc Natl Acad Sci U S A, 96, 9479-9484.
PDB code: 1qdl
10387029 Y.X.Fan, P.McPhie, and E.W.Miles (1999).
Guanidine hydrochloride exerts dual effects on the tryptophan synthase alpha 2 beta 2 complex as a cation activator and as a modulator of the active site conformation.
  Biochemistry, 38, 7881-7890.  
9562556 D.T.Gallagher, G.L.Gilliland, G.Xiao, J.Zondlo, K.E.Fisher, D.Chinchilla, and E.Eisenstein (1998).
Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase.
  Structure, 6, 465-475.
PDB code: 1tdj
9914248 J.L.Smith (1998).
Glutamine PRPP amidotransferase: snapshots of an enzyme in action.
  Curr Opin Struct Biol, 8, 686-694.  
9914259 J.N.Jansonius (1998).
Structure, evolution and action of vitamin B6-dependent enzymes.
  Curr Opin Struct Biol, 8, 759-769.  
9837895 K.D.Schnackerz, and A.Mozzarelli (1998).
Plasticity of the tryptophan synthase active site probed by 31P NMR spectroscopy.
  J Biol Chem, 273, 33247-33253.  
9565551 K.H.Jhee, L.H.Yang, S.A.Ahmed, P.McPhie, R.Rowlett, and E.W.Miles (1998).
Mutation of an active site residue of tryptophan synthase (beta-serine 377) alters cofactor chemistry.
  J Biol Chem, 273, 11417-11422.  
9772188 K.H.Jhee, P.McPhie, H.S.Ro, and E.W.Miles (1998).
Tryptophan synthase mutations that alter cofactor chemistry lead to mechanism-based inactivation.
  Biochemistry, 37, 14591-14604.  
9485448 R.Rowlett, L.H.Yang, S.A.Ahmed, P.McPhie, K.H.Jhee, and E.W.Miles (1998).
Mutations in the contact region between the alpha and beta subunits of tryptophan synthase alter subunit interaction and intersubunit communication.
  Biochemistry, 37, 2961-2968.  
9692955 S.Rhee, E.W.Miles, A.Mozzarelli, and D.R.Davies (1998).
Cryocrystallography and microspectrophotometry of a mutant (alpha D60N) tryptophan synthase alpha 2 beta 2 complex reveals allosteric roles of alpha Asp60.
  Biochemistry, 37, 10653-10659.
PDB code: 1beu
9535826 S.Rhee, E.W.Miles, and D.R.Davies (1998).
Cryo-crystallography of a true substrate, indole-3-glycerol phosphate, bound to a mutant (alphaD60N) tryptophan synthase alpha2beta2 complex reveals the correct orientation of active site alphaGlu49.
  J Biol Chem, 273, 8553-8555.
PDB codes: 1a5a 1a5b
9548921 T.R.Schneider, E.Gerhardt, M.Lee, P.H.Liang, K.S.Anderson, and I.Schlichting (1998).
Loop closure and intersubunit communication in tryptophan synthase.
  Biochemistry, 37, 5394-5406.
PDB codes: 1a50 1a5s 2wsy
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.