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| | ==Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-ADP== | | ==Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-ADP== |
| - | <StructureSection load='1kjq' size='340' side='right' caption='[[1kjq]], [[Resolution|resolution]] 1.05Å' scene=''> | + | <StructureSection load='1kjq' size='340' side='right'caption='[[1kjq]], [[Resolution|resolution]] 1.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1kjq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KJQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1kjq]] 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=1KJQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KJQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.05Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PURT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1kjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kjq OCA], [http://pdbe.org/1kjq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kjq RCSB], [http://www.ebi.ac.uk/pdbsum/1kjq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kjq 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=1kjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kjq OCA], [https://pdbe.org/1kjq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kjq RCSB], [https://www.ebi.ac.uk/pdbsum/1kjq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kjq ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PURT_ECOLI PURT_ECOLI]] Catalyzes two reactions: the first one is the production of beta-formyl glycinamide ribonucleotide (GAR) from formate, ATP and beta GAR; the second, a side reaction, is the production of acetyl phosphate and ADP from acetate and ATP.[HAMAP-Rule:MF_01643] | + | [https://www.uniprot.org/uniprot/PURT_ECOLI PURT_ECOLI] Catalyzes two reactions: the first one is the production of beta-formyl glycinamide ribonucleotide (GAR) from formate, ATP and beta GAR; the second, a side reaction, is the production of acetyl phosphate and ADP from acetate and ATP.[HAMAP-Rule:MF_01643] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Benkovic, S J]] | + | [[Category: Large Structures]] |
| - | [[Category: Firestine, S M]] | + | [[Category: Benkovic SJ]] |
| - | [[Category: Holden, H M]] | + | [[Category: Firestine SM]] |
| - | [[Category: Thoden, J B]] | + | [[Category: Holden HM]] |
| - | [[Category: Atp-grasp]] | + | [[Category: Thoden JB]] |
| - | [[Category: Nucleotide]]
| + | |
| - | [[Category: Purine biosynthesis]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
1kjq is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.05Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PURT_ECOLI Catalyzes two reactions: the first one is the production of beta-formyl glycinamide ribonucleotide (GAR) from formate, ATP and beta GAR; the second, a side reaction, is the production of acetyl phosphate and ADP from acetate and ATP.[HAMAP-Rule:MF_01643]
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
PurT-encoded glycinamide ribonucleotide transformylase, or PurT transformylase, functions in purine biosynthesis by catalyzing the formylation of glycinamide ribonucleotide through a catalytic mechanism requiring Mg(2+)ATP and formate. From previous x-ray diffraction analyses, it has been demonstrated that PurT transformylase from Escherichia coli belongs to the ATP-grasp superfamily of enzymes, which are characterized by three structural motifs referred to as the A-, B-, and C-domains. In all of the ATP-grasp enzymes studied to date, the adenosine nucleotide ligands are invariably wedged between the B- and C-domains, and in some cases, such as biotin carboxylase and carbamoyl phosphate synthetase, the B-domains move significantly upon nucleotide binding. Here we present a systematic and high-resolution structural investigation of PurT transformylase complexed with various adenosine nucleotides or nucleotide analogs including Mg(2+)ATP, Mg(2+)-5'-adenylylimidodiphosphate, Mg(2+)-beta,gamma-methyleneadenosine 5'-triphosphate, Mg(2+)ATPgammaS, or Mg(2+)ADP. Taken together, these studies indicate that the conformation of the so-called "T-loop," delineated by Lys-155 to Gln-165, is highly sensitive to the chemical identity of the nucleotide situated in the binding pocket. This sensitivity to nucleotide identity is in sharp contrast to that observed for the "P-loop"-containing enzymes, in which the conformation of the binding motif is virtually unchanged in the presence or absence of nucleotides.
PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site.,Thoden JB, Firestine SM, Benkovic SJ, Holden HM J Biol Chem. 2002 Jun 28;277(26):23898-908. Epub 2002 Apr 12. PMID:11953435[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Thoden JB, Firestine SM, Benkovic SJ, Holden HM. PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. J Biol Chem. 2002 Jun 28;277(26):23898-908. Epub 2002 Apr 12. PMID:11953435 doi:10.1074/jbc.M202251200
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