1m4t: Difference between revisions

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<StructureSection load='1m4t' size='340' side='right'caption='[[1m4t]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
<StructureSection load='1m4t' size='340' side='right'caption='[[1m4t]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1m4t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_19544 Atcc 19544]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M4T FirstGlance]. <br>
<table><tr><td colspan='2'>[[1m4t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Zoogloea_ramigera Zoogloea ramigera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M4T FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.77&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CY4:S-BUTYRYL-CYSTEIN'>CY4</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CY4:S-BUTYRYL-CYSTEIN'>CY4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dlu|1dlu]], [[1dlv|1dlv]], [[1qfl|1qfl]], [[1dm3|1dm3]], [[1m1o|1m1o]], [[1m1t|1m1t]], [[1m3z|1m3z]], [[1m4s|1m4s]]</div></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></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=1m4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4t OCA], [https://pdbe.org/1m4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m4t RCSB], [https://www.ebi.ac.uk/pdbsum/1m4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m4t ProSAT]</span></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=1m4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4t OCA], [https://pdbe.org/1m4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m4t RCSB], [https://www.ebi.ac.uk/pdbsum/1m4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m4t ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/THIL_SHIZO THIL_SHIZO]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1m4t 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=1m4t ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Biosynthetic thiolase catalyzes the formation of acetoacetyl-CoA from two molecules of acetyl-CoA. This is a key step in the synthesis of many biological compounds, including steroid hormones and ketone bodies. The thiolase reaction involves two chemically distinct steps; during acyl transfer, an acetyl group is transferred from acetyl-CoA to Cys89, and in the Claisen condensation step, this acetyl group is further transferred to a second molecule of acetyl-CoA, generating acetoacetyl-CoA. Here, new crystallographic data for Zoogloea ramigera biosynthetic thiolase are presented, covering all intermediates of the thiolase catalytic cycle. The high-resolution structures indicate that the acetyl group goes through four conformations while being transferred from acetyl-CoA via the acetylated enzyme to acetoacetyl-CoA. This transfer is catalyzed in a rigid cavity lined by mostly hydrophobic side chains, in addition to the catalytic residues Cys89, His348, and Cys378. The structures highlight the importance of an oxyanion hole formed by a water molecule and His348 in stabilizing the negative charge on the thioester oxygen atom of acetyl-CoA at two different steps of the reaction cycle. Another oxyanion hole, composed of the main chain nitrogen atoms of Cys89 and Gly380, complements a negative charge of the thioester oxygen anion of the acetylated intermediate, stabilizing the tetrahedral transition state of the Claisen condensation step. The reactivity of the active site may be modulated by hydrogen bonding networks extending from the active site toward the back of the molecule.
The catalytic cycle of biosynthetic thiolase: a conformational journey of an acetyl group through four binding modes and two oxyanion holes.,Kursula P, Ojala J, Lambeir AM, Wierenga RK Biochemistry. 2002 Dec 31;41(52):15543-56. PMID:12501183<ref>PMID:12501183</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1m4t" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Thiolase 3D structures|Thiolase 3D structures]]
*[[Thiolase 3D structures|Thiolase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Acetyl-CoA C-acetyltransferase]]
[[Category: Atcc 19544]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Kursula, P]]
[[Category: Zoogloea ramigera]]
[[Category: Lambeir, A M]]
[[Category: Kursula P]]
[[Category: Ojala, J]]
[[Category: Lambeir A-M]]
[[Category: Wierenga, R K]]
[[Category: Ojala J]]
[[Category: Butyrylated intermediate]]
[[Category: Wierenga RK]]
[[Category: Thiolase fold]]
[[Category: Transferase]]

Latest revision as of 11:31, 10 April 2024

Biosynthetic thiolase, Cys89 butyrylatedBiosynthetic thiolase, Cys89 butyrylated

Structural highlights

1m4t is a 4 chain structure with sequence from Zoogloea ramigera. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.77Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

THIL_SHIZO

Evolutionary Conservation

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

See Also

1m4t, resolution 1.77Å

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