2v9y

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[[Image:2v9y.gif|left|200px]]<br />
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[[Image:2v9y.jpg|left|200px]]<br /><applet load="2v9y" size="450" color="white" frame="true" align="right" spinBox="true"
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<applet load="2v9y" size="450" color="white" frame="true" align="right" spinBox="true"
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caption="2v9y, resolution 2.10&Aring;" />
caption="2v9y, resolution 2.10&Aring;" />
'''HUMAN AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE'''<br />
'''HUMAN AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE'''<br />
==Overview==
==Overview==
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BACKGROUND: The purine biosynthetic pathway in procaryotes enlists eleven, enzymes, six of which use ATP. Enzymes 5 and 6 of this pathway, formylglycinamide ribonucleotide (FGAR) amidotransferase (PurL) and, aminoimidazole ribonucleotide (AIR) synthetase (PurM) utilize ATP to, activate the oxygen of an amide within their substrate toward nucleophilic, attack by a nitrogen. AIR synthetase uses the product of PurL, formylglycinamidine ribonucleotide (FGAM) and ATP to make AIR, ADP and, P(i). RESULTS: The structure of a hexahistidine-tagged PurM has been, solved by multiwavelength anomalous diffraction phasing techniques using, protein containing 28 selenomethionines per asymmetric unit. The final, model of PurM consists of two crystallographically independent dimers and, four sulfates. The overall R factor at 2.5 A resolution is 19.2%, with an, R(free) of 26.4%. The active site, identified in part by conserved, residues, is proposed to be a long groove generated by the interaction of, two monomers. A search of the sequence databases suggests that the, ATP-binding sites between PurM and PurL may be structurally conserved., CONCLUSIONS: The first structure of a new class of ATP-binding enzyme, PurM, has been solved and a model for the active site has been proposed., The structure is unprecedented, with an extensive and unusual, sheet-mediated intersubunit interaction defining the active-site grooves., Sequence searches suggest that two successive enzymes in the purine, biosynthetic pathway, proposed to use similar chemistries, will have, similar ATP-binding domains.
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We tested the general applicability of in situ proteolysis to form protein, crystals suitable for structure determination by adding a protease, (chymotrypsin or trypsin) digestion step to crystallization trials of 55, bacterial and 14 human proteins that had proven recalcitrant to our best, efforts at crystallization or structure determination. This is a work in, progress; so far we determined structures of 9 bacterial proteins and the, human aminoimidazole ribonucleotide synthetase (AIRS) domain.
==About this Structure==
==About this Structure==
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2V9Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_cyclo-ligase Phosphoribosylformylglycinamidine cyclo-ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.1 6.3.3.1] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2V9Y OCA].
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2V9Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_cyclo-ligase Phosphoribosylformylglycinamidine cyclo-ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.1 6.3.3.1] Known structural/functional Sites: <scene name='pdbsite=AC1:So4 Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:So4 Binding Site For Chain B'>AC2</scene> and <scene name='pdbsite=AC3:So4 Binding Site For Chain B'>AC3</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2V9Y OCA].
==Reference==
==Reference==
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X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution., Li C, Kappock TJ, Stubbe J, Weaver TM, Ealick SE, Structure. 1999 Sep 15;7(9):1155-66. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10508786 10508786]
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In situ proteolysis for protein crystallization and structure determination., Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Leo RD, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P Jr, Flodin S, Flores A, Graslund S, Hammerstrom M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H, Nat Methods. 2007 Nov 4;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17982461 17982461]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Phosphoribosylformylglycinamidine cyclo-ligase]]
[[Category: Phosphoribosylformylglycinamidine cyclo-ligase]]
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[[Category: transferase]]
[[Category: transferase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 23:42:54 2007''
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 20:33:15 2007''

Revision as of 18:23, 18 December 2007

Image:2v9y.jpg

2v9y, resolution 2.10Å

Drag the structure with the mouse to rotate

HUMAN AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE

Overview

We tested the general applicability of in situ proteolysis to form protein, crystals suitable for structure determination by adding a protease, (chymotrypsin or trypsin) digestion step to crystallization trials of 55, bacterial and 14 human proteins that had proven recalcitrant to our best, efforts at crystallization or structure determination. This is a work in, progress; so far we determined structures of 9 bacterial proteins and the, human aminoimidazole ribonucleotide synthetase (AIRS) domain.

About this Structure

2V9Y is a Single protein structure of sequence from Homo sapiens with SO4 as ligand. Active as Phosphoribosylformylglycinamidine cyclo-ligase, with EC number 6.3.3.1 Known structural/functional Sites: , and . Full crystallographic information is available from OCA.

Reference

In situ proteolysis for protein crystallization and structure determination., Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Leo RD, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P Jr, Flodin S, Flores A, Graslund S, Hammerstrom M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H, Nat Methods. 2007 Nov 4;. PMID:17982461

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