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PDBsum entry 1rd5

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1rd5
Jmol
Contents
Protein chains
261 a.a. *
248 a.a. *
Ligands
MLA ×2
Waters ×248
* Residue conservation analysis
PDB id:
1rd5
Name: Lyase
Title: Crystal structure of tryptophan synthase alpha chain homolog member of the chemical plant defense system
Structure: Tryptophan synthase alpha chain, chloroplast. Chain: a, b. Synonym: bx1, tryptophan synthase alpha homolog. Engineered: yes
Source: Zea mays. Organism_taxid: 4577. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Octamer (from PQS)
Resolution:
2.02Å     R-factor:   0.248     R-free:   0.299
Authors: V.Kulik,E.Hartmann,M.Weyand,M.Frey,A.Gierl,D.Niks,M.F.Dunn, I.Schlichting
Key ref:
V.Kulik et al. (2005). On the structural basis of the catalytic mechanism and the regulation of the alpha subunit of tryptophan synthase from Salmonella typhimurium and BX1 from maize, two evolutionarily related enzymes. J Mol Biol, 352, 608-620. PubMed id: 16120446 DOI: 10.1016/j.jmb.2005.07.014
Date:
05-Nov-03     Release date:   28-Dec-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P42390  (TRPA_MAIZE) -  Indole-3-glycerol phosphate lyase, chloroplastic
Seq:
Struc:
347 a.a.
261 a.a.*
Protein chain
Pfam   ArchSchema ?
P42390  (TRPA_MAIZE) -  Indole-3-glycerol phosphate lyase, chloroplastic
Seq:
Struc:
347 a.a.
248 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chains A, B: E.C.4.1.2.8  - Indole-3-glycerol-phosphate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate
= indole
+
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = MLA)
matches with 41.67% similarity
   Enzyme class 2: Chains A, B: E.C.4.2.1.20  - Tryptophan synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + D-glyceraldehyde 3-phosphate + H2O
L-serine
Bound ligand (Het Group name = MLA)
matches with 75.00% similarity
+ 1-C-(indol-3-yl)glycerol 3-phosphate
= L-tryptophan
+ D-glyceraldehyde 3-phosphate
+ H(2)O
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
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!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.07.014 J Mol Biol 352:608-620 (2005)
PubMed id: 16120446  
 
 
On the structural basis of the catalytic mechanism and the regulation of the alpha subunit of tryptophan synthase from Salmonella typhimurium and BX1 from maize, two evolutionarily related enzymes.
V.Kulik, E.Hartmann, M.Weyand, M.Frey, A.Gierl, D.Niks, M.F.Dunn, I.Schlichting.
 
  ABSTRACT  
 
Indole is a reaction intermediate in at least two biosynthetic pathways in maize seedlings. In the primary metabolism, the alpha-subunit (TSA) of the bifunctional tryptophan synthase (TRPS) catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and d-glyceraldehyde 3-phosphate (G3P). Subsequently, indole diffuses through the connecting tunnel to the beta-active site where it is condensed with serine to form tryptophan and water. The maize enzyme, BX1, a homolog of TSA, also cleaves IGP to G3P and indole, and the indole is further converted to 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one, a secondary plant metabolite. BX1 cleaves IGP significantly faster to G3P and indole than does TSA. In line with their different biological functions, these two evolutionary related enzymes differ significantly in their regulatory aspects while catalyzing the same chemistry. Here, the mechanism of IGP cleavage by TSA was analyzed using a novel transition state analogue generated in situ by reaction of 2-aminophenol and G3P. The crystal structure of the complex shows an sp3-hybridized atom corresponding to the C3 position of IGP. The catalytic alphaGlu49 rotates to interact with the sp3-hybridized atom and the 3' hydroxyl group suggesting that it serves both as proton donor and acceptor in the alpha-reaction. The second catalytic residue, alphaAsp60 interacts with the atom corresponding to the indolyl nitrogen, and the catalytically important loop alphaL6 is in the closed, high activity conformation. Comparison of the TSA and TSA-transition state analogue structures with the crystal structure of BX1 suggests that the faster catalytic rate of BX1 may be due to a stabilization of the active conformation: loop alphaL6 is closed and the catalytic glutamate is in the active conformation. The latter is caused by a substitution of the residues that stabilize the inactive conformation in TRPS.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Environment of the catalytic glutamate. (a) In TPRS, aGlu49 has two conformations, an extended active one interacting with the 3'-hydroxyl of IGP and an inactive one with the carboxylate hydrogen bonded with aTyr173. (b) In BX1 (yellow), Glu134 is positioned in the active conformation. Due to a number of substitutions, including Phe253<->aTyr173 and Ile207<->aLeu127, the corresponding inactive conformation seen in TPRS is not energetically favorable in the BX1 structure.
Figure 7.
Figure 7. The conformation of loop aL6 is determined by the position of an arginine residue. (a) In a-TRPS, the guanidinium group of aArg179 lies in the plane of the loop and forms a number of radial interactions. (b) In BX1 the corresponding guanidinium group, Arg266, is tilted out of the ring plane, resulting in only one interaction with the loop. The two guanidinium groups occupy similar positions in space.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 608-620) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21085641 M.Q.Fatmi, and C.E.Chang (2010).
The role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase.
  PLoS Comput Biol, 6, e1000994.  
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.  
18366663 R.Merkl, and M.Zwick (2008).
H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.
  BMC Bioinformatics, 9, 151.  
18844775 R.Zhang, B.Wang, J.Ouyang, J.Li, and Y.Wang (2008).
Arabidopsis indole synthase, a homolog of tryptophan synthase alpha, is an enzyme involved in the Trp-independent indole-containing metabolite biosynthesis.
  J Integr Plant Biol, 50, 1070-1077.  
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
18430213 V.Kriechbaumer, L.Weigang, A.Fiesselmann, T.Letzel, M.Frey, A.Gierl, and E.Glawischnig (2008).
Characterisation of the tryptophan synthase alpha subunit in maize.
  BMC Plant Biol, 8, 44.  
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.