This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1r30

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:20, 14 February 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1r30.gif|left|200px]]
 
-
{{Structure
+
==The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme==
-
|PDB= 1r30 |SIZE=350|CAPTION= <scene name='initialview01'>1r30</scene>, resolution 3.40&Aring;
+
<StructureSection load='1r30' size='340' side='right'caption='[[1r30]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=DTB:6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC+ACID'>DTB</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
+
<table><tr><td colspan='2'>[[1r30]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R30 FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin_synthase Biotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.1.6 2.8.1.6] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.4&#8491;</td></tr>
-
|GENE= BIOB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTB:6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC+ACID'>DTB</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r30 OCA], [https://pdbe.org/1r30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r30 RCSB], [https://www.ebi.ac.uk/pdbsum/1r30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r30 ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r30 OCA], [http://www.ebi.ac.uk/pdbsum/1r30 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r30 RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/BIOB_ECOLI BIOB_ECOLI] Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism.<ref>PMID:8142361</ref>
-
 
+
== Evolutionary Conservation ==
-
'''The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r3/1r30_consurf.spt"</scriptWhenChecked>
-
The crystal structure of biotin synthase from Escherichia coli in complex with S-adenosyl-L-methionine and dethiobiotin has been determined to 3.4 angstrom resolution. This structure addresses how "AdoMet radical" or "radical SAM" enzymes use Fe4S4 clusters and S-adenosyl-L-methionine to generate organic radicals. Biotin synthase catalyzes the radical-mediated insertion of sulfur into dethiobiotin to form biotin. The structure places the substrates between the Fe4S4 cluster, essential for radical generation, and the Fe2S2 cluster, postulated to be the source of sulfur, with both clusters in unprecedented coordination environments.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1R30 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R30 OCA].
+
</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=1r30 ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
== References ==
-
Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme., Berkovitch F, Nicolet Y, Wan JT, Jarrett JT, Drennan CL, Science. 2004 Jan 2;303(5654):76-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14704425 14704425]
+
<references/>
-
[[Category: Biotin synthase]]
+
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Berkovitch, F.]]
+
[[Category: Berkovitch F]]
-
[[Category: Drennan, C L.]]
+
[[Category: Drennan CL]]
-
[[Category: Jarrett, J T.]]
+
[[Category: Jarrett JT]]
-
[[Category: Nicolet, Y.]]
+
[[Category: Nicolet Y]]
-
[[Category: Wan, J T.]]
+
[[Category: Wan JT]]
-
[[Category: fes cluster]]
+
-
[[Category: sam radical protein]]
+
-
[[Category: tim barrel]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:22:34 2008''
+

Current revision

The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme

PDB ID 1r30

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1r30"
Personal tools