4s29: Difference between revisions

Revision as of 10:40, 15 March 2023

Crystal structure of Arabidopsis thaliana ThiC with bound imidazole ribonucleotide and Fe

Structural highlights

4s29 is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	BU1, FE2, IRN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

THIC_ARATH Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.^[1] ^[2]

Publication Abstract from PubMed

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a beta-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the beta-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.,Fenwick MK, Mehta AP, Zhang Y, Abdelwahed SH, Begley TP, Ealick SE Nat Commun. 2015 Mar 27;6:6480. doi: 10.1038/ncomms7480. PMID:25813242^[3]

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

References

↑ Raschke M, Burkle L, Muller N, Nunes-Nesi A, Fernie AR, Arigoni D, Amrhein N, Fitzpatrick TB. Vitamin B1 biosynthesis in plants requires the essential iron sulfur cluster protein, THIC. Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19637-42. Epub 2007 Nov 28. PMID:18048325 doi:https://dx.doi.org/10.1073/pnas.0709597104
↑ Kong D, Zhu Y, Wu H, Cheng X, Liang H, Ling HQ. AtTHIC, a gene involved in thiamine biosynthesis in Arabidopsis thaliana. Cell Res. 2008 May;18(5):566-76. doi: 10.1038/cr.2008.35. PMID:18332905 doi:https://dx.doi.org/10.1038/cr.2008.35
↑ Fenwick MK, Mehta AP, Zhang Y, Abdelwahed SH, Begley TP, Ealick SE. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase. Nat Commun. 2015 Mar 27;6:6480. doi: 10.1038/ncomms7480. PMID:25813242 doi:https://dx.doi.org/10.1038/ncomms7480

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Raschke M, Burkle L, Muller N, Nunes-Nesi A, Fernie AR, Arigoni D, Amrhein N, Fitzpatrick TB. Vitamin B1 biosynthesis in plants requires the essential iron sulfur cluster protein, THIC. Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19637-42. Epub 2007 Nov 28. PMID:18048325 doi:https://dx.doi.org/10.1073/pnas.0709597104

[2] Kong D, Zhu Y, Wu H, Cheng X, Liang H, Ling HQ. AtTHIC, a gene involved in thiamine biosynthesis in Arabidopsis thaliana. Cell Res. 2008 May;18(5):566-76. doi: 10.1038/cr.2008.35. PMID:18332905 doi:https://dx.doi.org/10.1038/cr.2008.35

[3] Fenwick MK, Mehta AP, Zhang Y, Abdelwahed SH, Begley TP, Ealick SE. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase. Nat Commun. 2015 Mar 27;6:6480. doi: 10.1038/ncomms7480. PMID:25813242 doi:https://dx.doi.org/10.1038/ncomms7480

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='4s29' size='340' side='right'caption='[[4s29]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4s29]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4S29 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4s29]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4S29 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=IRN:1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE'>IRN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=IRN:1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE'>IRN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4n7q|4n7q]], [[3epm|3epm]], [[3epn|3epn]], [[3epo|3epo]], [[4s25|4s25]], [[4s26|4s26]], [[4s27|4s27]], [[4s28|4s28]], [[4s2a|4s2a]]</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=4s29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s29 OCA], [https://pdbe.org/4s29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4s29 RCSB], [https://www.ebi.ac.uk/pdbsum/4s29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4s29 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">THIC, PY, At2g29630, T27A16.27 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphomethylpyrimidine_synthase Phosphomethylpyrimidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.17 4.1.99.17] </span></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=4s29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s29 OCA], [http://pdbe.org/4s29 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4s29 RCSB], [http://www.ebi.ac.uk/pdbsum/4s29 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4s29 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/THIC_ARATH THIC_ARATH]] Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.<ref>PMID:18048325</ref> <ref>PMID:18332905</ref>
+[https://www.uniprot.org/uniprot/THIC_ARATH THIC_ARATH] Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.<ref>PMID:18048325</ref> <ref>PMID:18332905</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Phosphomethylpyrimidine synthase]]
+[[Category: Abdelwahed S]]
-[[Category: Abdelwahed, S]]
+[[Category: Begley TP]]
-[[Category: Begley, T P]]
+[[Category: Ealick SE]]
-[[Category: Ealick, S E]]
+[[Category: Fenwick MK]]
-[[Category: Fenwick, M K]]
+[[Category: Mehta AP]]
-[[Category: Mehta, A P]]
+[[Category: Zhang Y]]
-[[Category: Zhang, Y]]
-[[Category: Adomet and glutamate mutase]]
-[[Category: Alpha-beta barrel]]
-[[Category: Domain swapping]]
-[[Category: Iron-sulfur cluster]]
-[[Category: Lyase]]
-[[Category: Radical sam superfamily]]
-[[Category: Thiamin]]
-[[Category: Vitamin b1]]
-[[Category: Vitamin b12]]

4s29: Difference between revisions

Revision as of 10:40, 15 March 2023

Crystal structure of Arabidopsis thaliana ThiC with bound imidazole ribonucleotide and Fe

Structural highlights

Function

Publication Abstract from PubMed

References

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