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PDBsum entry 1w3i

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protein ligands Protein-protein interface(s) links
Aldolase PDB id
1w3i
Jmol
Contents
Protein chains
293 a.a. *
Ligands
PYR ×4
GOL ×10
Waters ×878
* Residue conservation analysis
PDB id:
1w3i
Name: Aldolase
Title: Sulfolobus solfataricus 2-keto-3-deoxygluconate (kdg) aldolase complex with pyruvate
Structure: 2-keto-3-deoxy gluconate aldolase. Chain: a, b, c, d. Synonym: eda. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.7Å     R-factor:   0.179     R-free:   0.211
Authors: A.Theodossis,H.Walden,E.J.Westwick,H.Connaris,H.J.Lamble, D.W.Hough,M.J.Danson,G.L.Taylor
Key ref:
A.Theodossis et al. (2004). The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus. J Biol Chem, 279, 43886-43892. PubMed id: 15265860 DOI: 10.1074/jbc.M407702200
Date:
15-Jul-04     Release date:   02-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O54288  (O54288_SULSF) -  2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase
Seq:
Struc:
294 a.a.
293 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.4.1.2.14  - 2-dehydro-3-deoxy-phosphogluconate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
2-dehydro-3-deoxy-6-phosphate-D-gluconate
= pyruvate
+ D-glyceraldehyde 3-phosphate
   Enzyme class 2: E.C.4.1.2.21  - 2-dehydro-3-deoxy-6-phosphogalactonate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate
2-dehydro-3-deoxy-6-phospho-D-galactonate
= pyruvate
+ D-glyceraldehyde 3-phosphate
   Enzyme class 3: E.C.4.1.2.51  - 2-dehydro-3-deoxy-D-gluconate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-dehydro-3-deoxy-D-gluconate = pyruvate + D-glyceraldehyde
2-dehydro-3-deoxy-D-gluconate
= pyruvate
+ D-glyceraldehyde
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     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M407702200 J Biol Chem 279:43886-43892 (2004)
PubMed id: 15265860  
 
 
The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus.
A.Theodossis, H.Walden, E.J.Westwick, H.Connaris, H.J.Lamble, D.W.Hough, M.J.Danson, G.L.Taylor.
 
  ABSTRACT  
 
The hyperthermophilic Archaea Sulfolobus solfataricus grows optimally above 80 degrees C and metabolizes glucose by a non-phosphorylative variant of the Entner-Doudoroff pathway. In this pathway glucose dehydrogenase and gluconate dehydratase catalyze the oxidation of glucose to gluconate and the subsequent dehydration of gluconate to D-2-keto-3-deoxygluconate (KDG). KDG aldolase (KDGA) then catalyzes the cleavage of KDG to D-glyceraldehyde and pyruvate. It has recently been shown that all the enzymes of this pathway exhibit a catalytic promiscuity that also enables them to be used for the metabolism of galactose. This phenomenon, known as metabolic pathway promiscuity, depends crucially on the ability of KDGA to cleave KDG and D-2-keto-3-deoxygalactonate (KDGal), in both cases producing pyruvate and D-glyceraldehyde. In turn, the aldolase exhibits a remarkable lack of stereoselectivity in the condensation reaction of pyruvate and D-glyceraldehyde, forming a mixture of KDG and KDGal. We now report the structure of KDGA, determined by multiwavelength anomalous diffraction phasing, and confirm that it is a member of the tetrameric N-acetylneuraminate lyase superfamily of Schiff base-forming aldolases. Furthermore, by soaking crystals of the aldolase at more than 80 degrees C below its temperature activity optimum, we have been able to trap Schiff base complexes of the natural substrates pyruvate, KDG, KDGal, and pyruvate plus D-glyceraldehyde, which have allowed rationalization of the structural basis of promiscuous substrate recognition and catalysis. It is proposed that the active site of the enzyme is rigid to keep its thermostability but incorporates extra functionality to be promiscuous.
 
  Selected figure(s)  
 
Figure 3.
FIG. 3. S. solfataricus KGDA catalytic mechanism. Suggested mechanism of KDGA based on that proposed for NAL, indicating the ability of the enzyme to accept substrates that vary at both stereocenters C-4 and C-5. Complexes trapped in this study are shown in bold.
Figure 4.
FIG. 4. Substrate-enzyme interactions. Schematic summary of interactions made with the diastereomers KDG and KDGal.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 43886-43892) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20826162 I.Campeotto, A.H.Bolt, T.A.Harman, C.Dennis, C.H.Trinh, S.E.Phillips, A.Nelson, A.R.Pearson, and A.Berry (2010).
Structural insights into substrate specificity in variants of N-acetylneuraminic Acid lyase produced by directed evolution.
  J Mol Biol, 404, 56-69.
PDB codes: 2wnn 2wnq 2wnz 2wo5 2wpb 2xfw
20023024 M.Reher, T.Fuhrer, M.Bott, and P.Schönheit (2010).
The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase.
  J Bacteriol, 192, 964-974.  
20235827 O.Khersonsky, and D.S.Tawfik (2010).
Enzyme promiscuity: a mechanistic and evolutionary perspective.
  Annu Rev Biochem, 79, 471-505.  
  19923724 I.Campeotto, S.B.Carr, C.H.Trinh, A.S.Nelson, A.Berry, S.E.Phillips, and A.R.Pearson (2009).
Structure of an Escherichia coli N-acetyl-D-neuraminic acid lyase mutant, E192N, in complex with pyruvate at 1.45 angstrom resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 1088-1090.
PDB code: 2wkj
  19478916 S.Wolterink-van Loo, M.A.Siemerink, G.Perrakis, T.Kaper, S.W.Kengen, and J.van der Oost (2009).
Improving low-temperature activity of Sulfolobus acidocaldarius 2-keto-3-deoxygluconate aldolase.
  Archaea, 2, 233-239.  
18230325 A.Bolt, A.Berry, and A.Nelson (2008).
Directed evolution of aldolases for exploitation in synthetic organic chemistry.
  Arch Biochem Biophys, 474, 318-330.  
18186475 A.Pauluhn, H.Ahmed, E.Lorentzen, S.Buchinger, D.Schomburg, B.Siebers, and E.Pohl (2008).
Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax.
  Proteins, 72, 35-43.
PDB codes: 2r91 2r94
19018105 J.A.Potter, M.Kerou, H.J.Lamble, S.D.Bull, D.W.Hough, M.J.Danson, and G.L.Taylor (2008).
The structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase.
  Acta Crystallogr D Biol Crystallogr, 64, 1283-1287.
PDB codes: 2v78 2var
18361457 S.Manicka, Y.Peleg, T.Unger, S.Albeck, O.Dym, H.M.Greenblatt, G.Bourenkov, V.Lamzin, S.Krishnaswamy, and J.L.Sussman (2008).
Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.
  Proteins, 71, 2102-2108.
PDB codes: 2v8z 2v9d
17549431 T.J.Ettema, H.Ahmed, A.C.Geerling, J.van der Oost, and B.Siebers (2008).
The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway.
  Extremophiles, 12, 75-88.  
17764545 D.Kehrer, H.Ahmed, H.Brinkmann, and B.Siebers (2007).
Glycerate kinase of the hyperthermophilic archaeon Thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes.
  BMC Genomics, 8, 301.  
  17565178 N.Shimada, B.Mikami, S.Watanabe, and K.Makino (2007).
Preliminary crystallographic analysis of L-2-keto-3-deoxyarabonate dehydratase, an enzyme involved in an alternative bacterial pathway of L-arabinose metabolism.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 393-395.  
  17565193 S.P.Kanaujia, C.V.Ranjani, J.Jeyakanthan, M.Nishida, Y.Kitamura, S.Baba, A.Ebihara, N.Shimizu, N.Nakagawa, A.Shinkai, M.Yamamoto, S.Kuramitsu, Y.Shiro, K.Sekar, and S.Yokoyama (2007).
Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 446-448.  
16287120 E.Blagova, V.Levdikov, N.Milioti, M.J.Fogg, A.K.Kalliomaa, J.A.Brannigan, K.S.Wilson, and A.J.Wilkinson (2006).
Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 A resolution.
  Proteins, 62, 297-301.
PDB codes: 1xky 1xl9
  16508107 A.Theodossis, C.C.Milburn, N.I.Heyer, H.J.Lamble, D.W.Hough, M.J.Danson, and G.L.Taylor (2005).
Preliminary crystallographic studies of glucose dehydrogenase from the promiscuous Entner-Doudoroff pathway in the hyperthermophilic archaeon Sulfolobus solfataricus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 112-115.  
16256419 B.Siebers, and P.Schönheit (2005).
Unusual pathways and enzymes of central carbohydrate metabolism in Archaea.
  Curr Opin Microbiol, 8, 695-705.  
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.