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| | ==N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI== | | ==N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI== |
| - | <StructureSection load='1b6r' size='340' side='right' caption='[[1b6r]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='1b6r' size='340' side='right'caption='[[1b6r]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1b6r]] is a 1 chain structure with 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=1B6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1b6r]] is a 1 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=1B6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B6R FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoribosylaminoimidazole_carboxylase Phosphoribosylaminoimidazole carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.21 4.1.1.21] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1b6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6r OCA], [http://pdbe.org/1b6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b6r RCSB], [http://www.ebi.ac.uk/pdbsum/1b6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b6r ProSAT]</span></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=1b6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6r OCA], [https://pdbe.org/1b6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b6r RCSB], [https://www.ebi.ac.uk/pdbsum/1b6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b6r ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PURK_ECOLI PURK_ECOLI]] Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR). | + | [https://www.uniprot.org/uniprot/PURK_ECOLI PURK_ECOLI] Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b6/1b6r_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b6/1b6r_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1b6r" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1b6r" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Phosphoribosylaminoimidazole carboxylase 3D structures|Phosphoribosylaminoimidazole carboxylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Phosphoribosylaminoimidazole carboxylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Holden, H M]] | + | [[Category: Holden HM]] |
| - | [[Category: Kappock, T J]] | + | [[Category: Kappock TJ]] |
| - | [[Category: Stubbe, J]] | + | [[Category: Stubbe J]] |
| - | [[Category: Thoden, J B]] | + | [[Category: Thoden JB]] |
| - | [[Category: Atp-grasp]]
| + | |
| - | [[Category: Carboxyphosphate]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Purine biosynthesis]]
| + | |
| Structural highlights
Function
PURK_ECOLI Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR).
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
Escherichia coli PurK, a dimeric N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. Crystallization of both a sulfate-liganded and the MgADP-liganded E. coli PurK has resulted in structures at 2.1 and 2.5 A resolution, respectively. PurK belongs to the ATP grasp superfamily of C-N ligase enzymes. Each subunit of PurK is composed of three domains (A, B, and C). The B domain contains a flexible, glycine-rich loop (B loop, T123-G130) that is disordered in the sulfate-PurK structure and becomes ordered in the MgADP-PurK structure. MgADP is wedged between the B and C domains, as with all members of the ATP grasp superfamily. Other enzymes in this superfamily contain a conserved Omega loop proposed to interact with the B loop, define the specificity of their nonnucleotide substrate, and protect the acyl phosphate intermediate formed from this substrate. PurK contains a minimal Omega loop without conserved residues. In the reaction catalyzed by PurK, carboxyphosphate is the putative acyl phosphate intermediate. The sulfate of the sulfate ion-liganded PurK interacts electrostatically with Arg 242 and the backbone amide group of Asn 245, components of the J loop of the C domain. This sulfate may reveal the location of the carboxyphosphate binding site. Conserved residues within the C-terminus of the C domain define a pocket that is proposed to bind AIR in collaboration with an N-terminal strand loop helix motif in the A domain (P loop, G8-L1). The P loop is proposed to bind the phosphate of AIR on the basis of similar binding sites observed in PurN and PurE and proposed in PurD and PurT, four other enzymes in the purine pathway.
Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily.,Thoden JB, Kappock TJ, Stubbe J, Holden HM Biochemistry. 1999 Nov 23;38(47):15480-92. PMID:10569930[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Thoden JB, Kappock TJ, Stubbe J, Holden HM. Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily. Biochemistry. 1999 Nov 23;38(47):15480-92. PMID:10569930
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