Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax

Proteins: Structure, Function and Genetics

Volumn 72, Issue 1, 2008, Pages 35-43

  Pauluhn, Anuschka ^a   Ahmed, Hatim ^b   Lorentzen, Esben ^c   Buchinger, Sebastian ^d   Schomburg, Dietmar ^e   Siebers, Bettina ^b   Pohl, Ehmke ^a,f  

^a PAUL SCHERRER INSTITUTE   (Switzerland)

^b UNIVERSITY OF DUISBURG ESSEN   (Germany)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^d UNIVERSITY OF COLOGNE   (Germany)

^e TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^f DURHAM UNIVERSITY   (United Kingdom)

Author keywords

Archaea; Embden Meyerhof Parnas pathway; Entner Doudoroff pathway; KD(P)GA; Stereo control

Indexed keywords

2 KETO 3 DEOXY (6 PHOSPHO) GLUCONATE ALDOLASE; 2 OXO 3 DEOXY 6 PHOSPHOGLUCONATE; 2 OXO 3 DEOXYGLUCONIC ACID; APOPROTEIN; FRUCTOSE BISPHOSPHATE ALDOLASE; GALACTOSE; GLUCONIC ACID; GLUCOSE; GLYCERALDEHYDE; PYRUVIC ACID;

ARTICLE; CARBOHYDRATE METABOLISM; CRYSTAL STRUCTURE; ENZYME DEGRADATION; EPIMER; GAS CHROMATOGRAPHY; HYPERTHERMOPHILIC ARCHAEON; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; STEREOCHEMISTRY; SULFOLOBUS SOLFATARICUS; THERMOACIDOPHILIC ARCHAEON; THERMOPROTEUS TENAX;

ALDEHYDE-LYASES; AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ELECTROSTATICS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GLUCONATES; ISOMERISM; LEAST-SQUARES ANALYSIS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PYRUVIC ACID; SEQUENCE ALIGNMENT; SULFOLOBUS SOLFATARICUS; THERMOPROTEUS;

CRENARCHAEOTA; SULFOLOBUS ACIDOCALDARIUS; SULFOLOBUS SOLFATARICUS; THERMOPROTEUS TENAX;

EID: 44949177497     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21890     Document Type: Article

References (37)

1. Rutter WJ. Evolution of aldolase. Fed Proc 1964;23:1248-1259.
2. 8 barrel proteins. J Biol Chem 2003;278:47253- 47260.
3. Samland AK, Sprenger GA. Microbial aldolases as C-C bonding enzymes - unknown treasures and new developments. Appl Microbiol Biotechnol 2006;71:253-264.
4. Thomson GJ, Howlett GJ, Ashcroft AE, Berry A. The dhna gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. Biochem J 1998;331:437-445.
5. Schürmann M, Sprenger GA. Fructose-6-phosphate aldolase is a novel class I aldolase from Escherichia coli and is related to a novel group of bacterial transaldolases. J Biol Chem 2001;276:11055-11061.
6. Siebers B, Brinkmann H, Dörr C, Tjaden B, Lilie H, van der Oost J, Verhees CH. Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase. J Biol Chem 2001;276:28710-28718.
7. Machajewski TD, Wong C. The catalytic asymmetric aldol reaction. Angew Chem Int Ed 2000;39:1352-1375.
8. Buchanan CL, Connaris H, Danson MJ, Reeve CD, Hough DW. An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for nonphosphorylated substrates. Biochem J 1999;343:563-570.
9. Babbitt PC, Gerlt JA. Understanding enzyme superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities. J Biol Chem 1997;272:30591-30594.
10. Theodossis A, Walden H, Westwick EJ, Connaris H, Lamble HJ, Hough DW, Danson MJ, Taylor GL. The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus. J Biol Chem 2004;279:43886-43892.
11. Wolterink-van Loo S, van Eerde A, Siemerink MAJ, Akerboom J, Dijkstra BW, van der Oost J. Biochemical and structural exploration of the catalytic capacity of sulfolobus KDG aldolases. Biochem J 2006.
12. Siebers B, Tjaden B, Michalke K, Dörr C, Ahmed H, Zaparty M, Gordon P, Sensen CW, Zibat A, Klenk HP, Schuster SC, Hensel R. Reconstruction of the central carbohydrate metabolism of Thermoproteus tenax by use of genomic and biochemical data. J Bact 2004;186:2179-2194.
13. Ahmed H, Ettema TJ, Tjaden B, Geerling AC, van der Oost J, Siebers B. The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation. Biochem J 2005;390:529-540.
14. Lamble HJ, Theodossis A, Milburn CC, Taylor GL, Bull SD, Hough DW, Danson MJ. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett 2005;579:6865-6869.
15. Lamble HJ, Heyer NI, Bull SD, Hough DW, Danson DW. Metabolic pathway promiscuity in the Archaeon Sulfolobus solfataricus revealed by studies on glucose dehydrogenase and 2-keto-3-deoxygluconate aldolase. J Biol Chem 2003;278:34066-34072.
16. Lamble HJ, Milburn CC, Taylor GL, Hough DW, Danson MJ. Gluconate dehydratase from the promiscuous Entner-Doudoroff pathway in Sulfolobus solfataricus. FEBS Lett 2004;576:133-136.
17. Zillig W, Stetter KO, Schäfer W, Jankovic D, Wunderl S, Holz I, Palm P. Thermoproteales: A novel type of extremely thermoacidophilic anaerobic archaebacteria isolated from icelandic solfatares. Zentbl Bakteriol Hyg 1 Abt Orig C 1981;2:205-227.
18. Siebers B, Wendisch VF, Hensel R. Carbohydrate metabolism in Thermoproteus tenax: In vivo utilization of the non-phosphorylative Entner-Doudoroff pathway and characterization of its first enzyme, glucose dehydrogenase. Arch Microbiol 1997;168:120-127.
19. van den Dool H, Kratz PD. A generalization of the retention index system including linear temperature programmed gas-liquid partition chromatography. J Chromatogr 1963;11:463-471.
20. Strelkov S, von Elstermann M, Schomburg D. Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry. Biol Chem 2004;385:853-861.
21. Pohl E, Pradervand C, Schneider R, Tomizaki T, Pauluhn A, Chen Q, Ingold G, Zimoch E, Schulze-Briese C. The new protein crystallography beamline X10SA at the Swiss Light Source. Synchrotr Rad News 2006;19:24-26.
22. Kabsch W. Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J Appl Cryst Dec 1988;21:916-924.
23. McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ. Likelihood-enhanced fast translation functions. Acta Cryst D 2005;61:458-464.
24. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
25. Matthews BW. Solvent content of protein crystals. J Mol Biol 1968;33:491-497.
26. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst D 1997;53:240-255.
27. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Cryst D 2004;60:2126-2132.
28. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
29. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Cryst D 1994;50:760-763.
30. Brunger AT. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992;355:472-475.
31. Jones S, Thornton JM. Principles of protein-protein interactions derived from structural studies. Proc Natl Acad Sci 1996;93:13-20.
32. Jaenicke R, Bohm G. The stability of proteins in extreme environments. Curr Opin Struct Biol 1998;8:738-748.
33. Pohl E, Brunner N, Wilmanns M, Hensel R. The crystal structure of the allosteric non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeum Thermoproteus tenax. J Biol Chem 2002;277:19938-19945.
34. Lokanath NK, Shiromizu I, Ohshima N, Nodake Y, Sugahara M, Yokoyama S, Kuramitsu S, Miyano M, Kunishima N. Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability. Acta Cryst D 2004;60:1816-1823.
35. Walden H, Taylor GL, Lorentzen E, Pohl E, Lilie H, Schramm A, Knura T, Stubbe K, Tjaden B, Hensel R. Structure and function of a regulated archaeal triosephosphate isomerase adapted to high temperature. J Mol Biol 2004;342:861-875.
36. Smith BJ, Lawrence MC, Barbosa JA. Substrate-assisted catalysis in sialic acid aldolase. J Org Chem 1999;64:945-949.
37. O'Brien PJ, Herschlag D. Catalytic promiscuity and the evolution of new enzymatic activities. Chem Biol 1999;6:R91-R105.