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PDBsum entry 1onr

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protein Protein-protein interface(s) links
Transferase PDB id
1onr
Jmol
Contents
Protein chains
316 a.a. *
Waters ×524
* Residue conservation analysis
PDB id:
1onr
Name: Transferase
Title: Structure of transaldolase b
Structure: Transaldolase b. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.87Å     R-factor:   0.201     R-free:   0.234
Authors: J.Jia,W.Huang,Y.Lindqvist,G.Schneider
Key ref:
J.Jia et al. (1996). Crystal structure of transaldolase B from Escherichia coli suggests a circular permutation of the alpha/beta barrel within the class I aldolase family. Structure, 4, 715-724. PubMed id: 8805555
Date:
13-Aug-96     Release date:   12-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A870  (TALB_ECOLI) -  Transaldolase B
Seq:
Struc:
317 a.a.
316 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.2.1.2  - Transaldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate
Sedoheptulose 7-phosphate
+ D-glyceraldehyde 3-phosphate
= D-erythrose 4-phosphate
+ D-fructose 6-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
Structure 4:715-724 (1996)
PubMed id: 8805555  
 
 
Crystal structure of transaldolase B from Escherichia coli suggests a circular permutation of the alpha/beta barrel within the class I aldolase family.
J.Jia, W.Huang, U.Schörken, H.Sahm, G.A.Sprenger, Y.Lindqvist, G.Schneider.
 
  ABSTRACT  
 
BACKGROUND: Transaldolase is one of the enzymes in the non-oxidative branch of the pentose phosphate pathway. It transfers a C3 ketol fragment from a ketose donor to an aldose acceptor. Transaldolase, together with transketolase, creates a reversible link between the pentose phosphate pathway and glycolysis. The enzyme is of considerable interest as a catalyst in stereospecific organic synthesis and the aim of this work was to reveal the molecular architecture of transaldolase and provide insights into the structural basis of the enzymatic mechanism. RESULTS: The three-dimensional (3D) structure of recombinant transaldolase B from E. coli was determined at 1.87 A resolution. The enzyme subunit consists of a single eight-stranded alpha/beta-barrel domain. Two subunits form a dimer related by a twofold symmetry axis. The active-site residue Lys132 which forms a Schiff base with the substrate is located at the bottom of the active-site cleft. CONCLUSIONS: The 3D structure of transaldolase is similar to structures of other enzymes in the class I aldolase family. Comparison of these structures suggests that a circular permutation of the protein sequence might have occurred in transaldolase, which nevertheless results in a similar 3D structure. This observation provides evidence for a naturally occurring circular permutation in an alpha/beta-barrel protein. It appears that such genetic permutations occur more frequently during evolution than was previously thought.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20934451 D.W.Song, J.G.Lee, H.S.Youn, S.H.Eom, and d.o. .H.Kim (2011).
Ryanodine receptor assembly: A novel systems biology approach to 3D mapping.
  Prog Biophys Mol Biol, 105, 145-161.  
21290439 M.Rale, S.Schneider, G.A.Sprenger, A.K.Samland, and W.D.Fessner (2011).
Broadening deoxysugar glycodiversity: natural and engineered transaldolases unlock a complementary substrate space.
  Chemistry, 17, 2623-2632.  
19401148 A.K.Samland, and G.A.Sprenger (2009).
Transaldolase: from biochemistry to human disease.
  Int J Biochem Cell Biol, 41, 1482-1494.  
18318840 A.K.Samland, M.Wang, and G.A.Sprenger (2008).
MJ0400 from Methanocaldococcus jannaschii exhibits fructose-1,6-bisphosphate aldolase activity.
  FEMS Microbiol Lett, 281, 36-41.  
18831051 H.Huang, H.Rong, X.Li, S.Tong, Z.Zhu, L.Niu, and M.Teng (2008).
The crystal structure and identification of NQM1/YGR043C, a transaldolase from Saccharomyces cerevisiae.
  Proteins, 73, 1076-1081.
PDB code: 3cq0
18687684 S.Schneider, T.Sandalova, G.Schneider, G.A.Sprenger, and A.K.Samland (2008).
Replacement of a Phenylalanine by a Tyrosine in the Active Site Confers Fructose-6-phosphate Aldolase Activity to the Transaldolase of Escherichia coli and Human Origin.
  J Biol Chem, 283, 30064-30072.
PDB code: 3cwn
16447159 K.J.Taylor-McCabe, Z.Wang, N.N.Sauer, and B.L.Marrone (2006).
Proteomic analysis of beryllium-induced genotoxicity in an Escherichia coli mutant model system.
  Proteomics, 6, 1663-1675.  
16651269 Y.Nishitani, D.Maruyama, T.Nonaka, A.Kita, T.A.Fukami, T.Mio, H.Yamada-Okabe, T.Yamada-Okabe, and K.Miki (2006).
Crystal structures of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, and its substrate and product complexes.
  J Biol Chem, 281, 19740-19747.
PDB codes: 2dka 2dkc 2dkd
15840824 D.R.Livesay, and D.La (2005).
The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins.
  Protein Sci, 14, 1158-1170.  
15960612 M.Caillau, and W.Paul Quick (2005).
New insights into plant transaldolase.
  Plant J, 43, 1.  
  15215359 C.Guda, S.Lu, E.D.Scheeff, P.E.Bourne, and I.N.Shindyalov (2004).
CE-MC: a multiple protein structure alignment server.
  Nucleic Acids Res, 32, W100-W103.  
  15810435 T.Soderberg, and R.C.Alver (2004).
Transaldolase of Methanocaldococcus jannaschii.
  Archaea, 1, 255-262.  
12842039 B.N.Chaudhuri, M.R.Sawaya, C.Y.Kim, G.S.Waldo, M.S.Park, T.C.Terwilliger, and T.O.Yeates (2003).
The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.
  Structure, 11, 753-764.
PDB code: 1oy0
12941964 E.Lorentzen, E.Pohl, P.Zwart, A.Stark, R.B.Russell, T.Knura, R.Hensel, and B.Siebers (2003).
Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins.
  J Biol Chem, 278, 47253-47260.
PDB codes: 1ojx 1ok4 1ok6
12151227 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Plasticity of enzyme active sites.
  Trends Biochem Sci, 27, 419-426.  
11779856 A.Maurady, A.Zdanov, D.de Moissac, D.Beaudry, and J.Sygusch (2002).
A conserved glutamate residue exhibits multifunctional catalytic roles in D-fructose-1,6-bisphosphate aldolases.
  J Biol Chem, 277, 9474-9483.
PDB codes: 1ewd 1ewe 1ewg 1ex5 3b8d
  11514678 J.Jung, and B.Lee (2001).
Circularly permuted proteins in the protein structure database.
  Protein Sci, 10, 1881-1886.  
11342129 N.Wymer, L.V.Buchanan, D.Henderson, N.Mehta, C.H.Botting, L.Pocivavsek, C.A.Fierke, E.J.Toone, and J.H.Naismith (2001).
Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli.
  Structure, 9, 1-9.
PDB codes: 1fq0 1fwr
11298760 U.Schörken, S.Thorell, M.Schürmann, J.Jia, G.A.Sprenger, and G.Schneider (2001).
Identification of catalytically important residues in the active site of Escherichia coli transaldolase.
  Eur J Biochem, 268, 2408-2415.
PDB codes: 1i2n 1i2o 1i2p 1i2q 1i2r
  10048322 A.Dalby, Z.Dauter, and J.A.Littlechild (1999).
Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: mechanistic implications.
  Protein Sci, 8, 291-297.
PDB codes: 2ald 4ald
9593194 S.García-Vallvé, A.Rojas, J.Palau, and A.Romeu (1998).
Circular permutants in beta-glucosidases (family 3) within a predicted double-domain topology that includes a (beta/alpha)8-barrel.
  Proteins, 31, 214-223.  
9667911 W.D.Fessner (1998).
Enzyme mediated C-C bond formation.
  Curr Opin Chem Biol, 2, 85-97.  
  9007983 J.Jia, U.Schörken, Y.Lindqvist, G.A.Sprenger, and G.Schneider (1997).
Crystal structure of the reduced Schiff-base intermediate complex of transaldolase B from Escherichia coli: mechanistic implications for class I aldolases.
  Protein Sci, 6, 119-124.
PDB code: 1ucw
9204286 Y.Lindqvist, and G.Schneider (1997).
Circular permutations of natural protein sequences: structural evidence.
  Curr Opin Struct Biol, 7, 422-427.  
8939754 S.J.Cooper, G.A.Leonard, S.M.McSweeney, A.W.Thompson, J.H.Naismith, S.Qamar, A.Plater, A.Berry, and W.N.Hunter (1996).
The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold.
  Structure, 4, 1303-1315.
PDB code: 1zen
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.