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PDBsum entry 2fpb

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protein ligands Protein-protein interface(s) links
Lyase PDB id
2fpb
Jmol
Contents
Protein chains
305 a.a. *
Ligands
TSS ×2
Waters ×173
* Residue conservation analysis
PDB id:
2fpb
Name: Lyase
Title: Structure of strictosidine synthase, the biosynthetic entry monoterpenoid indole alkaloid family
Structure: Strictosidine synthase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Rauvolfia serpentina. Serpentwood. Organism_taxid: 4060. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.80Å     R-factor:   0.166     R-free:   0.217
Authors: S.Panjikar
Key ref: X.Ma et al. (2006). The structure of Rauvolfia serpentina strictosidine synthase is a novel six-bladed beta-propeller fold in plant proteins. Plant Cell, 18, 907-920. PubMed id: 16531499 DOI: 10.1105/tpc.105.038018
Date:
16-Jan-06     Release date:   23-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P68175  (STSY_RAUSE) -  Strictosidine synthase
Seq:
Struc:
344 a.a.
305 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.3.3.2  - Strictosidine synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Indole and Ipecac Alkaloid Biosynthesis
      Reaction: 3-alpha-(S)-strictosidine + H2O = tryptamine + secologanin
3-alpha-(S)-strictosidine
+ H(2)O
=
tryptamine
Bound ligand (Het Group name = TSS)
corresponds exactly
+ secologanin
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     vacuole   1 term 
  Biological process     biosynthetic process   2 terms 
  Biochemical function     lyase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1105/tpc.105.038018 Plant Cell 18:907-920 (2006)
PubMed id: 16531499  
 
 
The structure of Rauvolfia serpentina strictosidine synthase is a novel six-bladed beta-propeller fold in plant proteins.
X.Ma, S.Panjikar, J.Koepke, E.Loris, J.Stöckigt.
 
  ABSTRACT  
 
The enzyme strictosidine synthase (STR1) from the Indian medicinal plant Rauvolfia serpentina is of primary importance for the biosynthetic pathway of the indole alkaloid ajmaline. Moreover, STR1 initiates all biosynthetic pathways leading to the entire monoterpenoid indole alkaloid family representing an enormous structural variety of approximately 2000 compounds in higher plants. The crystal structures of STR1 in complex with its natural substrates tryptamine and secologanin provide structural understanding of the observed substrate preference and identify residues lining the active site surface that contact the substrates. STR1 catalyzes a Pictet-Spengler-type reaction and represents a novel six-bladed beta-propeller fold in plant proteins. Structure-based sequence alignment revealed a common repetitive sequence motif (three hydrophobic residues are followed by a small residue and a hydrophilic residue), indicating a possible evolutionary relationship between STR1 and several sequence-unrelated six-bladed beta-propeller structures. Structural analysis and site-directed mutagenesis experiments demonstrate the essential role of Glu-309 in catalysis. The data will aid in deciphering the details of the reaction mechanism of STR1 as well as other members of this enzyme family.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20730220 L.Yang, and J.Stöckigt (2010).
Trends for diverse production strategies of plant medicinal alkaloids.
  Nat Prod Rep, 27, 1469-1479.  
20064432 H.Y.Lee, N.Yerkes, and S.E.O'Connor (2009).
Aza-tryptamine substrates in monoterpene indole alkaloid biosynthesis.
  Chem Biol, 16, 1225-1229.  
19219013 K.S.Ryan, and B.S.Moore (2009).
Alkaloid biosynthesis takes root.
  Nat Chem Biol, 5, 140-141.  
19844641 K.Yonekura-Sakakibara, and K.Saito (2009).
Functional genomics for plant natural product biosynthesis.
  Nat Prod Rep, 26, 1466-1487.  
19795053 P.Bernhardt, N.Yerkes, and S.E.O'Connor (2009).
Bypassing stereoselectivity in the early steps of alkaloid biosynthesis.
  Org Biomol Chem, 7, 4166-4168.  
19151732 W.Runguphan, and S.E.O'Connor (2009).
Metabolic reprogramming of periwinkle plant culture.
  Nat Chem Biol, 5, 151-153.  
18987991 Y.Lu, H.Wang, W.Wang, Z.Qian, L.Li, J.Wang, G.Zhou, and G.Kai (2009).
Molecular characterization and expression analysis of a new cDNA encoding strictosidine synthase from Ophiorrhiza japonica.
  Mol Biol Rep, 36, 1845-1852.  
18081287 J.J.Maresh, L.A.Giddings, A.Friedrich, E.A.Loris, S.Panjikar, B.L.Trout, J.Stöckigt, B.Peters, and S.E.O'Connor (2008).
Strictosidine synthase: mechanism of a Pictet-Spengler catalyzing enzyme.
  J Am Chem Soc, 130, 710-723.
PDB code: 2vaq
18251710 J.Ziegler, and P.J.Facchini (2008).
Alkaloid biosynthesis: metabolism and trafficking.
  Annu Rev Plant Biol, 59, 735-769.  
18476877 P.J.Facchini, and V.De Luca (2008).
Opium poppy and Madagascar periwinkle: model non-model systems to investigate alkaloid biosynthesis in plants.
  Plant J, 54, 763-784.  
17719485 B.O.Bachmann (2007).
Foundations for directed alkaloid biosynthesis.
  Chem Biol, 14, 875-876.  
17884630 E.A.Loris, S.Panjikar, M.Ruppert, L.Barleben, M.Unger, H.Schübel, and J.Stöckigt (2007).
Structure-based engineering of strictosidine synthase: auxiliary for alkaloid libraries.
  Chem Biol, 14, 979-985.
PDB code: 2v91
18033585 J.Stöckigt, and S.Panjikar (2007).
Structural biology in plant natural product biosynthesis--architecture of enzymes from monoterpenoid indole and tropane alkaloid biosynthesis.
  Nat Prod Rep, 24, 1382-1400.  
17668090 M.C.Galan, E.McCoy, and S.E.O'Connor (2007).
Chemoselective derivatization of alkaloids in periwinkle.
  Chem Commun (Camb), (), 3249-3251.  
17719488 P.Bernhardt, E.McCoy, and S.E.O'Connor (2007).
Rapid identification of enzyme variants for reengineered alkaloid biosynthesis in periwinkle.
  Chem Biol, 14, 888-897.  
  17142919 C.Rosenthal, U.Mueller, S.Panjikar, L.Sun, M.Ruppert, Y.Zhao, and J.Stöckigt (2006).
Expression, purification, crystallization and preliminary X-ray analysis of perakine reductase, a new member of the aldo-keto reductase enzyme superfamily from higher plants.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1286-1289.  
16874388 S.E.O'Connor, and J.J.Maresh (2006).
Chemistry and biology of monoterpene indole alkaloid biosynthesis.
  Nat Prod Rep, 23, 532-547.  
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.