The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase

Structure

Volumn 10, Issue 11, 2002, Pages 1475-1487

  Keller, Jacob P ^a   Smith, Paul M ^a   Benach, Jordi ^a   Christendat, Dinesh ^b   De Titta, George T ^c   Hunt, John F ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b UNIVERSITY HEALTH NETWORK   (Canada)

^c HAUPTMAN WOODWARD MEDICAL RESEARCH INSTITUTE   (United States)

Author keywords

Decarboxylase; Methyltransferase; S adenosyl methionine; Structural genomics; Structure based function assignment; Vitamin B12

Indexed keywords

BACTERIAL PROTEIN; CARBOXYLYASE; METHYLTRANSFERASE; PROTEIN CBIT; PROTEIN MTO146; S ADENOSYLMETHIONINE; UNCLASSIFIED DRUG; PRECORRIN 8W METHYLTRANSFERASE; PRECORRIN-8W METHYLTRANSFERASE;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME ACTIVITY; HYDROGEN BOND; METHANOBACTERIUM THERMOAUTOTROPHICUM; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; AMINO ACID SEQUENCE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; DIMERIZATION; METABOLISM; METHANOBACTERIUM; MOLECULAR CLONING; MOLECULAR GENETICS; PROMOTER REGION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); METHANOBACTERIUM; METHANOTHERMOBACTER THERMAUTOTROPHICUS;

AMINO ACID SEQUENCE; BINDING SITES; CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; METHANOBACTERIUM; METHYLTRANSFERASES; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; S-ADENOSYLMETHIONINE; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0036848698     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(02)00876-6     Document Type: Article

References (44)

1. Battersby A.R. How nature builds the pigments of life. the conquest of vitamin B12 Science. 264:1994;1551-1557.
2. Roth J.R., Lawrence J.G., Bobik T.A. Cobalamin (coenzyme B12). synthesis and biological significance Annu. Rev. Microbiol. 50:1996;137-181.
3. Roessner C.A., Spencer J.B., Stolowich N.J., Wang J., Nayar G.P., Santander P.J., Pichon C., Min C., Holderman M.T., Scott A.I. Genetically engineered synthesis of precorrin-6x and the complete corrinoid, hydrogenobyrinic acid, an advanced precursor of vitamin B12. Chem. Biol. 1:1994;119-124.
4. Santander P.J., Roessner C.A., Stolowich N.J., Holderman M.T., Scott A.I. How corrinoids are synthesized without oxygen. nature's first pathway to vitamin B12 Chem. Biol. 4:1997;659-666.
5. Raux E., Schubert H.L., Warren M.J. Biosynthesis of cobalamin (vitamin B12). a bacterial conundrum Cell. Mol. Life Sci. 57:2000;1880-1893.
6. Schubert H.L., Raux E., Wilson K.S., Warren M.J. Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis. Biochemistry. 38:1999;10660-10669.
7. Blanche F., Famechon A., Thibaut D., Debussche L., Cameron B., Crouzet J. Biosynthesis of vitamin B12 in Pseudomonas denitrificans. the biosynthetic sequence from precorrin-6y to precorrin-8x is catalyzed by the cobL gene product J. Bacteriol. 174:1992;1050-1052.
8. Raux E., Lanois A., Warren M.J., Rambach A., Thermes C. Cobalamin (vitamin B12) biosynthesis. identification and characterization of a Bacillus megaterium cobI operon Biochem. J. 335:1998;159-166.
9. Raux E., Schubert H.L., Roper J.M., Wilson K.S., Warren M.J. Vitamin B12. insights into biosynthesis's Mount Improbable Bioorg. Chem. 27:1999;100-118.
10. Lo Conte L., Brenner S.E., Hubbard T.J., Chothia C., Murzin A.G. SCOP database in 2002. refinements accommodate structural genomics Nucleic Acids Res. 30:2002;264-267.
11. Weiss V.H., McBride A.E., Soriano M.A., Filman D.J., Silver P.A., Hogle J.M. The structure and oligomerization of the yeast arginine methyltransferase, Hmt1. Nat. Struct. Biol. 7:2000;1165-1171.
12. Vidgren J., Svensson L.A., Liljas A. Crystal structure of catechol O-methyltransferase. Nature. 368:1994;354-358.
13. Spencer J.B., Stolowich N.J., Roessner C.A., Scott A.I. The Escherichia coli cysG gene encodes the multifunctional protein, siroheme synthase. FEBS Lett. 335:1993;57-60.
14. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST. a new generation of protein database search programs Nucleic Acids Res. 25:1997;3389-3402.
15. Hendrickson W.A. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science. 254:1991;51-58.
16. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
17. Cowtan K.D., Zhang K.Y. Density modification for macromolecular phase improvement. Prog. Biophys. Mol. Biol. 72:1999;245-270.
18. Navaza J. Implementation of molecular replacement in AMoRe. Acta Crystallogr. D Biol. Crystallogr. 57:2001;1367-1372.
19. Branden C., Tooze J. Introduction to Protein Structure. 1991;Garland, New York.
20. Holm L., Sander C. Dali. a network tool for protein structure comparison Trends Biochem. Sci. 20:1995;478-480.
21. Korolev S., Ikeguchi Y., Skarina T., Beasley S., Arrowsmith C., Edwards A., Joachimiak A., Pegg A.E., Savchenko A. The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat. Struct. Biol. 9:2002;27-31.
22. Schubert H.L., Wilson K.S., Raux E., Woodcock S.C., Warren M.J. The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase. Nat. Struct. Biol. 5:1998;585-592.
23. Blanche F., Debussche L., Thibaut D., Crouzet J., Cameron B. Purification and characterization of S-adenosyl-L-methionine. uroporphyrinogen III methyltransferase from Pseudomonas denitrificans J. Bacteriol. 171:1989;4222-4231.
24. Raux E., Schubert H.L., Woodcock S.C., Wilson K.S., Warren M.J. Cobalamin (vitamin B12) biosynthesis - cloning, expression and crystallisation of the Bacillus megaterium S-adenosyl-L-methionine- dependent cobalt-precorrin-4 transmethylase CbiF. Eur. J. Biochem. 254:1998;341-346.
25. Tran P.H., Korszun Z.R., Cerritelli S., Springhorn S.S., Lacks S.A. Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S- adenosylmethionine. Structure. 6:1998;1563-1575.
26. Carugo O., Argos P. NADP-dependent enzymes. I. Conserved stereochemistry of cofactor binding Proteins. 28:1997;10-28.
27. Shipman L.W., Li D., Roessner C.A., Scott A.I., Sacchettini J.C. Crystal structure of precorrin-8x methyl mutase. Structure. 9:2001;587-596.
28. Kumar S., Horton J.R., Jones G.D., Walker R.T., Roberts R.J., Cheng X. DNA containing 4′-thio-2′-deoxycytidine inhibits methylation by HhaI methyltransferase. Nucleic Acids Res. 25:1997;2773-2783.
29. Akhtar M., Abboud M.M., Barnard G., Jordan P., Zaman Z. Mechanism and stereochemistry of enzymic reactions involved in porphyrin biosynthesis. Philos. Trans. R. Soc. Lond. B Biol. Sci. 273:1976;117-136.
30. Martins B.M., Grimm B., Mock H.P., Huber R., Messerschmidt A. Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum. Implications for the catalytic mechanism. J. Biol. Chem. 276:2001;44108-44116.
31. Rossmann M.G., Adams M.J., Buehner M., Ford G.C., Hackert M.L., Liljas A., Rao S.T., Banaszak L.J., Hill E., Tsernoglou D.et al. Letter. molecular symmetry axes and subunit interfaces in certain dehydrogenases J. Mol. Biol. 76:1973;533-537.
32. Hendrickson W.A., Horton J.R., LeMaster D.M. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD). a vehicle for direct determination of three-dimensional structure EMBO J. 9:1990;1665-1672.
33. Terwilliger T.C., Berendzen J. Automated structure solution for MIR and MAD. Acta Crystallogr. D Biol. Crystallogr. 55:1999;849-861.
34. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
35. Brunger A.T. Free R value. a novel statistical quantity for assessing the accuracy of crystal structures Nature. 355:1992;472-475.
36. Engh R.A., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A. 47:1991;392-400.
37. Kraulis P.J. Molscript. a program to produce both detailed and schematic plots of proteins J. Appl. Crystallogr. 24:1991;946-950.
38. Esnouf R.M. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. Model. 15:1997;132-134., 112-113.
39. Merritt E.A., Bacon D.J. Raster3D. Photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.
40. Nicholls A., Sharp K., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins Struct. Funct. Genet. 11:1991;281-296.
41. Higgins D.G., Thompson J.D., Gibson T.J. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266:1996;383-402.
42. Wilmot C.M., Thornton J.M. Beta-turns and their distortions. a proposed new nomenclature Protein Eng. 3:1990;479-493.
43. Drenth J. Principles of Protein X-Ray Crystallography. 1994;Springer, New York.
44. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. Procheck. a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26:1993;283-291.