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PDBsum entry 1i7q

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1i7q
Jmol
Contents
Protein chains
517 a.a. *
192 a.a. *
Ligands
BEZ ×2
PYR ×2
GLU ×2
Metals
_MG ×2
Waters ×1324
* Residue conservation analysis
PDB id:
1i7q
Name: Lyase
Title: Anthranilate synthase from s. Marcescens
Structure: Anthranilate synthase. Chain: a, c. Synonym: anthranilate synthase trpe. Engineered: yes. Trpg. Chain: b, d. Synonym: anthranilate synthase trpg. Engineered: yes
Source: Serratia marcescens. Organism_taxid: 615. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
1.95Å     R-factor:   0.181     R-free:   0.246
Authors: G.Spraggon,C.Kim,X.Nguyen-Huu,M.-C.Yee,C.Yanofsky,S.E.Mills
Key ref:
G.Spraggon et al. (2001). The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan. Proc Natl Acad Sci U S A, 98, 6021-6026. PubMed id: 11371633 DOI: 10.1073/pnas.111150298
Date:
10-Mar-01     Release date:   16-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00897  (TRPE_SERMA) -  Anthranilate synthase component 1
Seq:
Struc:
519 a.a.
517 a.a.*
Protein chains
Pfam   ArchSchema ?
P00900  (TRPG_SERMA) -  Anthranilate synthase component 2
Seq:
Struc:
193 a.a.
192 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.4.1.3.27  - Anthranilate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Tryptophan Biosynthesis
      Reaction: Chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate
Chorismate
+
L-glutamine
Bound ligand (Het Group name = GLU)
matches with 90.00% similarity
=
anthranilate
Bound ligand (Het Group name = BEZ)
matches with 90.00% similarity
+
pyruvate
Bound ligand (Het Group name = PYR)
corresponds exactly
+ L-glutamate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     protein binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.111150298 Proc Natl Acad Sci U S A 98:6021-6026 (2001)
PubMed id: 11371633  
 
 
The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan.
G.Spraggon, C.Kim, X.Nguyen-Huu, M.C.Yee, C.Yanofsky, S.E.Mills.
 
  ABSTRACT  
 
The crystal structure of anthranilate synthase (AS) from Serratia marcescens, a mesophilic bacterium, has been solved in the presence of its substrates, chorismate and glutamine, and one product, glutamate, at 1.95 A, and with its bound feedback inhibitor, tryptophan, at 2.4 A. In comparison with the AS structure from the hyperthermophile Sulfolobus solfataricus, the S. marcescens structure shows similar subunit structures but a markedly different oligomeric organization. One crystal form of the S. marcescens enzyme displays a bound pyruvate as well as a putative anthranilate (the nitrogen group is ambiguous) in the TrpE subunit. It also confirms the presence of a covalently bound glutamyl thioester intermediate in the TrpG subunit. The tryptophan-bound form reveals that the inhibitor binds at a site distinct from that of the substrate, chorismate. Bound tryptophan appears to prevent chorismate binding by a demonstrable conformational effect, and the structure reveals how occupancy of only one of the two feedback inhibition sites can immobilize the catalytic activity of both TrpE subunits. The presence of effectors in the structure provides a view of the locations of some of the amino acid residues in the active sites. Our findings are discussed in terms of the previously described AS structure of S. solfataricus, mutational data obtained from enteric bacteria, and the enzyme's mechanism of action.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Structure of the AS of S. marcescens. (a) Ribbon diagram of the AS oligomer, TrpG subunits shown in blue, TrpE subdomain I shown in green subdomain II in yellow. Striped regions correspond to additional structure in S. marcescens compared with that of S. solfataricus. Glutamyl, benzoate, pyruvate, and tryptophan are shown as CPK models. (b) Stereo diagram of the heterodimer; TrpG shown in lilac, TrpE in black; regions of TrpG that move on addition of tryptophan relative the C-crystal are shown in red, whereas those of TrpE are in yellow; residues important to the CA-binding pocket (G328, T329, H398, G485) are shown as light blue balls, residues involved in pyruvate interactions (Y449, R469, G483) are in purple, residues involved in magnesium coordination (E358,361, E495, E498) are colored light purple, magnesium ion in orange, water molecules in dark blue, Trp-binding residues (S40, P291, M293, V453, Y455) are light green, and residues involved in glutamine binding (P57, G58, G60, C85, L86, Q89, S135, S136) are in green. Benzoate, pyruvate, magnesium, and glutamyl are shown as ball-and-stick figures. Produced by BOBSCRIPT and RASTER 3D (39-42).
Figure 3.
Fig. 3. Substrate product and Trp-binding sites of the AS molecule. Carbon atoms are dark gray, nitrogen blue, and oxygen red. Electrostatic and hydrogen-bond interactions are shown as black dotted lines. (a) Binding residues for glutamyl thioester intermediate of TrpG. Glutamyl moiety drawn with cyan bonds. A [A]-weighted F[o] F[c] map contoured at 3.5 SD is shown in transparent blue. (b) CA-binding pocket, anthranilate, and pyruvate are drawn with dark red bonds, magnesium ion in orange, ordered waters in cyan. A [A]-weighted F[o] F[c] map contoured at 3.0 SD is shown in transparent green. (c) Trp-binding pocket, tryptophan shown in green. (d) Conformational states associated with anthranilate, pyruvate, and Trp-bound forms. The molecule is viewed with the molecular 2-fold perpendicular to the page (i.e., perpendicular to the view in Fig. 2a). TrpG subunits shown in transparent blue, helixes and loops involved in heterotetramer rearrangement shown as rods, C-crystal representation shown in green rearrangement in the T-crystal, shown in red. Tryptophan is shown as CPK model in yellow. Produced by BOBSCRIPT and RASTER 3D (39-42).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21134639 J.M.Lipchock, and J.P.Loria (2010).
Nanometer propagation of millisecond motions in V-type allostery.
  Structure, 18, 1596-1607.  
20532401 R.J.Payne, E.M.Bulloch, O.Kerbarh, and C.Abell (2010).
Inhibition of chorismate-utilising enzymes by 2-amino-4-carboxypyridine and 4-carboxypyridone and 5-carboxypyridone analogues.
  Org Biomol Chem, 8, 3534-3542.  
19462053 R.J.Payne, E.M.Bulloch, M.M.Toscano, M.A.Jones, O.Kerbarh, and C.Abell (2009).
Synthesis and evaluation of 2,5-dihydrochorismate analogues as inhibitors of the chorismate-utilising enzymes.
  Org Biomol Chem, 7, 2421-2429.  
18458150 E.J.Hart, and S.G.Powers-Lee (2008).
Mutation analysis of carbamoyl phosphate synthetase: does the structurally conserved glutamine amidotransferase triad act as a functional dyad?
  Protein Sci, 17, 1120-1128.  
18597481 M.Morar, A.A.Hoskins, J.Stubbe, and S.E.Ealick (2008).
Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formation.
  Biochemistry, 47, 7816-7830.
PDB code: 3d54
17993537 N.J.Wierckx, H.Ballerstedt, J.A.de Bont, J.H.de Winde, H.J.Ruijssenaars, and J.Wery (2008).
Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: genetic and physiological basis for improved production.
  J Bacteriol, 190, 2822-2830.  
18182490 S.G.Van Lanen, S.Lin, and B.Shen (2008).
Biosynthesis of the enediyne antitumor antibiotic C-1027 involves a new branching point in chorismate metabolism.
  Proc Natl Acad Sci U S A, 105, 494-499.  
17898895 D.E.Scott, A.Ciulli, and C.Abell (2007).
Coenzyme biosynthesis: enzyme mechanism, structure and inhibition.
  Nat Prod Rep, 24, 1009-1026.  
17335098 O.Kerbarh, A.Ciulli, D.Y.Chirgadze, T.L.Blundell, and C.Abell (2007).
Nucleophile selectivity of chorismate-utilizing enzymes.
  Chembiochem, 8, 622-624.  
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
16923875 A.J.Harrison, M.Yu, T.Gårdenborg, M.Middleditch, R.J.Ramsay, E.N.Baker, and J.S.Lott (2006).
The structure of MbtI from Mycobacterium tuberculosis, the first enzyme in the biosynthesis of the siderophore mycobactin, reveals it to be a salicylate synthase.
  J Bacteriol, 188, 6081-6091.
PDB code: 2g5f
15770625 E.M.Bulloch, and C.Abell (2005).
Detection of covalent intermediates formed in the reaction of 4-amino-4-deoxychorismate synthase.
  Chembiochem, 6, 832-834.  
16010361 R.J.Payne, M.D.Toscano, E.M.Bulloch, A.D.Abell, and C.Abell (2005).
Design and synthesis of aromatic inhibitors of anthranilate synthase.
  Org Biomol Chem, 3, 2271-2281.  
15889161 R.J.Payne, O.Kerbarh, R.N.Miguel, A.D.Abell, and C.Abell (2005).
Inhibition studies on salicylate synthase.
  Org Biomol Chem, 3, 1825-1827.  
15511226 F.A.Lunn, and S.L.Bearne (2004).
Alternative substrates for wild-type and L109A E. coli CTP synthases: kinetic evidence for a constricted ammonia tunnel.
  Eur J Biochem, 271, 4204-4212.  
15296735 M.Goto, R.Omi, N.Nakagawa, I.Miyahara, and K.Hirotsu (2004).
Crystal structures of CTP synthetase reveal ATP, UTP, and glutamine binding sites.
  Structure, 12, 1413-1423.
PDB codes: 1vcm 1vcn 1vco
14997577 R.Schwarzenbacher, A.M.Deacon, L.Jaroszewski, L.S.Brinen, J.M.Canaves, X.Dai, M.A.Elsliger, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, M.S.Nelson, J.Ouyang, R.Page, A.Robb, K.Quijano, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, G.Wolf, K.O.Hodgson, J.Wooley, and I.A.Wilson (2004).
Crystal structure of a putative glutamine amido transferase (TM1158) from Thermotoga maritima at 1.7 A resolution.
  Proteins, 54, 801-805.
PDB code: 1o1y
15235940 W.M.Byrnes, and V.L.Vilker (2004).
Extrinsic factors potassium chloride and glycerol induce thermostability in recombinant anthranilate synthase from Archaeoglobus fulgidus.
  Extremophiles, 8, 455-462.  
12595723 M.Goto, R.Omi, J.Hoseki, N.Nakagawa, I.Miyahara, and K.Hirotsu (2003).
Expression, purification and preliminary X-ray characterization of CTP synthetase from Thermus thermophilus HB8.
  Acta Crystallogr D Biol Crystallogr, 59, 551-553.  
11839304 A.Douangamath, M.Walker, S.Beismann-Driemeyer, M.C.Vega-Fernandez, R.Sterner, and M.Wilmanns (2002).
Structural evidence for ammonia tunneling across the (beta alpha)(8) barrel of the imidazole glycerol phosphate synthase bienzyme complex.
  Structure, 10, 185-193.
PDB codes: 1gpw 1k9v
11841211 J.F.Parsons, P.Y.Jensen, A.S.Pachikara, A.J.Howard, E.Eisenstein, and J.E.Ladner (2002).
Structure of Escherichia coli aminodeoxychorismate synthase: architectural conservation and diversity in chorismate-utilizing enzymes.
  Biochemistry, 41, 2198-2208.
PDB codes: 1k0e 1k0g
12093726 O.Mayans, A.Ivens, L.J.Nissen, K.Kirschner, and M.Wilmanns (2002).
Structural analysis of two enzymes catalysing reverse metabolic reactions implies common ancestry.
  EMBO J, 21, 3245-3254.
PDB codes: 1gxb 1o17
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.