1v9a: Difference between revisions

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[[Image:1v9a.png|left|200px]]


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==Crystal structure of Uroporphyrin-III C-methyl transferase from Thermus thermophilus complexed with S-adenyl homocysteine==
The line below this paragraph, containing "STRUCTURE_1v9a", creates the "Structure Box" on the page.
<StructureSection load='1v9a' size='340' side='right'caption='[[1v9a]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1v9a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9A FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
{{STRUCTURE_1v9a|  PDB=1v9a  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9a OCA], [https://pdbe.org/1v9a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9a RCSB], [https://www.ebi.ac.uk/pdbsum/1v9a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9a ProSAT], [https://www.topsan.org/Proteins/RSGI/1v9a TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q5SKH6_THET8 Q5SKH6_THET8]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v9/1v9a_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1v9a ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Uroporphyrinogen-III C-methyltransferase from Thermus thermophilus is a multifunctional protein responsible for two of the eight S-adenosyl-methionine-dependent methylations of the corrin ring during vitamin B(12) synthesis. The structure of this protein has been solved to 2.0 A resolution in both the apo and cofactor-bound form. The monomer consists of two domains, A and B, each consisting of a five-stranded beta-sheet and two or three alpha-helices, with the cofactor bound at the interface. The biological unit is the dimer found in the asymmetric unit. This dimer is related by a non-crystallographic twofold such that two B domains combine to form a long ten-stranded beta-sheet. When compared with solved related structures, this structure shows clear differences in the region involved in cofactor and substrate binding, affirming the role of several previously implicated residues and questioning others. The solved related structures are characterized by an exposed active site. The T. thermophilus structure has this site restricted by the interaction of a flexible loop structure with a highly conserved residue, suggesting a mechanistic role. This structure represents the ;closed' form of the protein.


===Crystal structure of Uroporphyrin-III C-methyl transferase from Thermus thermophilus complexed with S-adenyl homocysteine===
Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus.,Rehse PH, Kitao T, Tahirov TH Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):913-9. Epub 2005, Jun 24. PMID:15983414<ref>PMID:15983414</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_15983414}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1v9a" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15983414 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15983414}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1V9A is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9A OCA].
[[Category: Thermus thermophilus HB8]]
 
[[Category: Kitao T]]
==Reference==
[[Category: Rehse PH]]
Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus., Rehse PH, Kitao T, Tahirov TH, Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):913-9. Epub 2005, Jun 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15983414 15983414]
[[Category: Tahirov TH]]
[[Category: Single protein]]
[[Category: Thermus thermophilus]]
[[Category: Uroporphyrinogen-III C-methyltransferase]]
[[Category: Kitao, T.]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Rehse, P H.]]
[[Category: Tahirov, T H.]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:05:24 2008''

Latest revision as of 10:50, 25 October 2023

Crystal structure of Uroporphyrin-III C-methyl transferase from Thermus thermophilus complexed with S-adenyl homocysteineCrystal structure of Uroporphyrin-III C-methyl transferase from Thermus thermophilus complexed with S-adenyl homocysteine

Structural highlights

1v9a is a 2 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

Q5SKH6_THET8

Evolutionary Conservation

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

Publication Abstract from PubMed

Uroporphyrinogen-III C-methyltransferase from Thermus thermophilus is a multifunctional protein responsible for two of the eight S-adenosyl-methionine-dependent methylations of the corrin ring during vitamin B(12) synthesis. The structure of this protein has been solved to 2.0 A resolution in both the apo and cofactor-bound form. The monomer consists of two domains, A and B, each consisting of a five-stranded beta-sheet and two or three alpha-helices, with the cofactor bound at the interface. The biological unit is the dimer found in the asymmetric unit. This dimer is related by a non-crystallographic twofold such that two B domains combine to form a long ten-stranded beta-sheet. When compared with solved related structures, this structure shows clear differences in the region involved in cofactor and substrate binding, affirming the role of several previously implicated residues and questioning others. The solved related structures are characterized by an exposed active site. The T. thermophilus structure has this site restricted by the interaction of a flexible loop structure with a highly conserved residue, suggesting a mechanistic role. This structure represents the ;closed' form of the protein.

Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus.,Rehse PH, Kitao T, Tahirov TH Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):913-9. Epub 2005, Jun 24. PMID:15983414[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Rehse PH, Kitao T, Tahirov TH. Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus. Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):913-9. Epub 2005, Jun 24. PMID:15983414 doi:10.1107/S0907444905008838

1v9a, resolution 2.00Å

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