title: X-ray structures of isopentenyl phosphate kinase.
abstract: Isoprenoid compounds are ubiquitous in nature, participating in important biological phenomena such as signal transduction, aerobic cellular respiration, photosynthesis, insect communication, and many others. They are derived from the 5-carbon isoprenoid substrates isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). In Archaea and Eukarya, these building blocks are synthesized via the mevalonate pathway. However, the genes required to convert mevalonate phosphate (MP) to IPP are missing in several species of Archaea. An enzyme with isopentenyl phosphate kinase (IPK) activity was recently discovered in Methanocaldococcus jannaschii (MJ), suggesting a departure from the classical sequence of converting MP to IPP. We have determined the high-resolution crystal structures of isopentenyl phosphate kinases in complex with both substrates and products from Thermoplasma acidophilum (THA), as well as the IPK from Methanothermobacter thermautotrophicus (MTH), by means of single-wavelength anomalous diffraction (SAD) and molecular replacement. A histidine residue (His50) in THA IPK makes a hydrogen bond with the terminal phosphates of IP and IPP, poising these molecules for phosphoryl transfer through an in-line geometry. Moreover, a lysine residue (Lys14) makes hydrogen bonds with nonbridging oxygen atoms at P(alpha) and P(gamma) and with the P(beta)-P(gamma) bridging oxygen atom in ATP. These interactions suggest a transition-state-stabilizing role for this residue. Lys14 is a part of a newly discovered "lysine triangle" catalytic motif in IPKs that also includes Lys5 and Lys205. Moreover, His50, Lys5, Lys14, and Lys205 are conserved in all IPKs and can therefore serve as fingerprints for identifying new homologues.
authors.affiliation: Department of Chemistry, University of Utah, Salt Lake City, 84112, USA.
authors.forename: Mark F
authors.initials: MF
authors.lastname: Mabanglo
authors.forename: Heidi L
authors.initials: HL
authors.lastname: Schubert
authors.forename: Mo
authors.initials: M
authors.lastname: Chen
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Hill
authors.forename: C Dale
authors.initials: CD
authors.lastname: Poulter
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D053898:Biosynthetic Pathways; D018360:Crystallography, X-Ray / Q000379:methods; D045782:Hemiterpenes / Q000096:biosynthesis / Q000737:chemistry; D006860:Hydrogen Bonding; D017013:Methanobacteriaceae / Q000201:enzymology; D008958:Models, Molecular; D011487:Protein Conformation; D011494:Protein Kinases / Q000737:chemistry / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013822:Thermoplasma / Q000201:enzymology
chemical_list: D019843:Archaeal Proteins; D045782:Hemiterpenes; D011494:Protein Kinases; C402428:isopentenyl monophosphate kinase
references.citation: Bioinformatics. 2000 Jun;16(6):566-7
references.pmid: 10980157
references.citation: J Biol Chem. 2005 Jul 8;280(27):25533-40
references.pmid: 15857829
references.citation: J Mol Biol. 2007 Sep 21;372(3):774-97
references.pmid: 17681537
references.citation: Genome Res. 2000 Oct;10(10):1468-84
references.pmid: 11042147
references.citation: Structure. 2002 Mar;10(3):329-42
references.pmid: 12005432
references.citation: J Biol Chem. 2008 Oct 17;283(42):28518-26
references.pmid: 18701452
references.citation: J Bacteriol. 2006 May;188(9):3192-8
references.pmid: 16621811
references.citation: Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3044-8
references.pmid: 8159703
references.citation: Protein Expr Purif. 2005 May;41(1):207-34
references.pmid: 15915565
references.citation: Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
references.pmid: 15299374
references.citation: Eur J Biochem. 2002 Jul;269(14):3339-54
references.pmid: 12135472
references.citation: J Mol Biol. 2007 Apr 13;367(5):1431-46
references.pmid: 17321544
references.citation: J Mol Biol. 2003 Aug 1;331(1):231-44
references.pmid: 12875848
references.citation: Biotechnol Bioeng. 2004 Jul 20;87(2):200-12
references.pmid: 15236249
references.citation: J Biol Chem. 2008 Jun 6;283(23):16216-25
references.pmid: 18334478
references.citation: Protein Sci. 1999 Apr;8(4):934-40
references.pmid: 10211841
references.citation: J Mol Biol. 2005 Sep 16;352(2):438-54
references.pmid: 16095620
references.citation: Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55
references.pmid: 15299926
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83
references.pmid: 17452350
references.citation: Methods Enzymol. 1997;276:307-26
references.pmid: 27754618
references.citation: Mol Microbiol. 2004 Apr;52(2):515-27
references.pmid: 15066037
references.citation: Biosci Biotechnol Biochem. 2002 Aug;66(8):1619-27
references.pmid: 12353619
references.citation: Bioorg Chem. 2004 Oct;32(5):292-308
references.pmid: 15381396
references.citation: Chem Rev. 1998 Jun 18;98(4):1263-1276
references.pmid: 11848932
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references.pmid: 15572765
references.citation: Biochemistry. 2010 Jan 12;49(1):207-17
references.pmid: 19928876
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
references.pmid: 20124702
references.citation: J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
references.pmid: 19461840
references.citation: Science. 1997 Sep 19;277(5333):1788-9
references.pmid: 9324768
references.citation: Biophys Chem. 2002 Jan 23;95(1):79-90
references.pmid: 11880175