3bg5: Difference between revisions

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[[Image:3bg5.png|left|200px]]


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==Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase==
The line below this paragraph, containing "STRUCTURE_3bg5", creates the "Structure Box" on the page.
<StructureSection load='3bg5' size='340' side='right'caption='[[3bg5]], [[Resolution|resolution]] 2.80&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'>[[3bg5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BG5 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]] 2.8&#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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=BTI:5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL'>BTI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
{{STRUCTURE_3bg5|  PDB=3bg5  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bg5 OCA], [https://pdbe.org/3bg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bg5 RCSB], [https://www.ebi.ac.uk/pdbsum/3bg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bg5 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PYC_STAAM PYC_STAAM] Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second.<ref>PMID:19523900</ref> <ref>PMID:23286247</ref>
== 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/bg/3bg5_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=3bg5 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pyruvate carboxylase (PC) catalyzes the biotin-dependent production of oxaloacetate and has important roles in gluconeogenesis, lipogenesis, insulin secretion and other cellular processes. PC contains the biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) domains. We report here the crystal structures at 2.8-A resolution of full-length PC from Staphylococcus aureus and the C-terminal region (missing only the BC domain) of human PC. A conserved tetrameric association is observed for both enzymes, and our structural and mutagenesis studies reveal a previously uncharacterized domain, the PC tetramerization (PT) domain, which is important for oligomerization. A BCCP domain is located in the active site of the CT domain, providing the first molecular insights into how biotin participates in the carboxyltransfer reaction. There are dramatic differences in domain positions in the monomer and the organization of the tetramer between these enzymes and the PC from Rhizobium etli.


===Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase===
Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.,Xiang S, Tong L Nat Struct Mol Biol. 2008 Mar;15(3):295-302. Epub 2008 Feb 24. PMID:18297087<ref>PMID:18297087</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3bg5" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18297087}}, adds the Publication Abstract to the page
*[[Pyruvate carboxylase 3D structures|Pyruvate carboxylase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18297087 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_18297087}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3BG5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BG5 OCA].
 
==Reference==
Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction., Xiang S, Tong L, Nat Struct Mol Biol. 2008 Mar;15(3):295-302. Epub 2008 Feb 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18297087 18297087]
[[Category: Single protein]]
[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
[[Category: Tong, L.]]
[[Category: Tong L]]
[[Category: Xiang, S.]]
[[Category: Xiang S]]
[[Category: Atp-binding]]
[[Category: Ligase]]
[[Category: Nucleotide-binding]]
[[Category: Pyruvate]]
[[Category: Tim barrel]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 08:47:55 2008''

Latest revision as of 11:53, 15 November 2023

Crystal Structure of Staphylococcus Aureus Pyruvate CarboxylaseCrystal Structure of Staphylococcus Aureus Pyruvate Carboxylase

Structural highlights

3bg5 is a 4 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYC_STAAM Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second.[1] [2]

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

Pyruvate carboxylase (PC) catalyzes the biotin-dependent production of oxaloacetate and has important roles in gluconeogenesis, lipogenesis, insulin secretion and other cellular processes. PC contains the biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) domains. We report here the crystal structures at 2.8-A resolution of full-length PC from Staphylococcus aureus and the C-terminal region (missing only the BC domain) of human PC. A conserved tetrameric association is observed for both enzymes, and our structural and mutagenesis studies reveal a previously uncharacterized domain, the PC tetramerization (PT) domain, which is important for oligomerization. A BCCP domain is located in the active site of the CT domain, providing the first molecular insights into how biotin participates in the carboxyltransfer reaction. There are dramatic differences in domain positions in the monomer and the organization of the tetramer between these enzymes and the PC from Rhizobium etli.

Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.,Xiang S, Tong L Nat Struct Mol Biol. 2008 Mar;15(3):295-302. Epub 2008 Feb 24. PMID:18297087[3]

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

See Also

References

  1. ↑ Yu LP, Xiang S, Lasso G, Gil D, Valle M, Tong L. A symmetrical tetramer for S. aureus pyruvate carboxylase in complex with coenzyme A. Structure. 2009 Jun 10;17(6):823-32. PMID:19523900 doi:10.1016/j.str.2009.04.008
  2. ↑ Yu LP, Chou CY, Choi PH, Tong L. Characterizing the Importance of the Biotin Carboxylase Domain Dimer for Staphylococcus aureus Pyruvate Carboxylase Catalysis. Biochemistry. 2013 Jan 9. PMID:23286247 doi:http://dx.doi.org/10.1021/bi301294d
  3. ↑ Xiang S, Tong L. Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction. Nat Struct Mol Biol. 2008 Mar;15(3):295-302. Epub 2008 Feb 24. PMID:18297087 doi:10.1038/nsmb.1393

3bg5, resolution 2.80Å

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