3ll5: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 1: Line 1:


==Crystal structure of T. acidophilum isopentenyl phosphate kinase product complex==
==Crystal structure of T. acidophilum isopentenyl phosphate kinase product complex==
<StructureSection load='3ll5' size='340' side='right' caption='[[3ll5]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
<StructureSection load='3ll5' size='340' side='right'caption='[[3ll5]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ll5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Theac Theac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LL5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LL5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ll5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum_DSM_1728 Thermoplasma acidophilum DSM 1728]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LL5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=IP8:ISOPENTENYL+PHOSPHATE'>IP8</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.987&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=IP8:ISOPENTENYL+PHOSPHATE'>IP8</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3lkk|3lkk]], [[3ll9|3ll9]]</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ll5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ll5 OCA], [https://pdbe.org/3ll5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ll5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ll5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ll5 ProSAT]</span></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ta0103 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273075 THEAC])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ll5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ll5 OCA], [http://pdbe.org/3ll5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ll5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ll5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ll5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IPK_THEAC IPK_THEAC] Catalyzes the formation of isopentenyl diphosphate (IPP), the building block of all isoprenoids. Has lower activity with isopentenyl thiolophosphate (ISP). Has low activity with dimethylallyl phosphate (DMAP), 1-butyl phosphate (BP) and 3-buten-1-yl phosphate (BEP). Has no significant activity with geranyl phosphate (in vitro).<ref>PMID:19928876</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 20: Line 20:
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ll5 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ll5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
X-ray structures of isopentenyl phosphate kinase.,Mabanglo MF, Schubert HL, Chen M, Hill CP, Poulter CD ACS Chem Biol. 2010 May 21;5(5):517-27. PMID:20402538<ref>PMID:20402538</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ll5" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Theac]]
[[Category: Large Structures]]
[[Category: Hill, C P]]
[[Category: Thermoplasma acidophilum DSM 1728]]
[[Category: Mabanglo, M F]]
[[Category: Hill CP]]
[[Category: Alpha-beta-alpha sandwich fold]]
[[Category: Mabanglo MF]]
[[Category: Alternate mevalonate pathway]]
[[Category: Isopentenyl phsophate kinase]]
[[Category: Kinase]]
[[Category: Product complex]]
[[Category: Transferase]]

Revision as of 09:40, 3 April 2024

Crystal structure of T. acidophilum isopentenyl phosphate kinase product complexCrystal structure of T. acidophilum isopentenyl phosphate kinase product complex

Structural highlights

3ll5 is a 4 chain structure with sequence from Thermoplasma acidophilum DSM 1728. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.987Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IPK_THEAC Catalyzes the formation of isopentenyl diphosphate (IPP), the building block of all isoprenoids. Has lower activity with isopentenyl thiolophosphate (ISP). Has low activity with dimethylallyl phosphate (DMAP), 1-butyl phosphate (BP) and 3-buten-1-yl phosphate (BEP). Has no significant activity with geranyl phosphate (in vitro).[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Chen M, Poulter CD. Characterization of thermophilic archaeal isopentenyl phosphate kinases. Biochemistry. 2010 Jan 12;49(1):207-17. PMID:19928876 doi:10.1021/bi9017957

3ll5, resolution 1.99Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=3ll5&oldid=4118937"