2gcq
From Proteopedia
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|PDB= 2gcq |SIZE=350|CAPTION= <scene name='initialview01'>2gcq</scene>, resolution 2.0Å | |PDB= 2gcq |SIZE=350|CAPTION= <scene name='initialview01'>2gcq</scene>, resolution 2.0Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DOI:9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-(PHOSPHONOOXY)-9H-PURINE'>DOI</scene>, <scene name='pdbligand=GDP:GUANOSINE-5'-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=HAD:(CARBOXYHYDROXYAMINO)ETHANOIC+ACID'>HAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Adenylosuccinate_synthase Adenylosuccinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.4 6.3.4.4] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylosuccinate_synthase Adenylosuccinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.4 6.3.4.4] </span> |
|GENE= purA, adeK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= purA, adeK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gcq OCA], [http://www.ebi.ac.uk/pdbsum/2gcq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2gcq RCSB]</span> | ||
}} | }} | ||
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[[Category: Honzatko, R B.]] | [[Category: Honzatko, R B.]] | ||
[[Category: Zhou, Y.]] | [[Category: Zhou, Y.]] | ||
| - | [[Category: | + | [[Category: 2'-deoxy-imp]] |
| - | [[Category: | + | [[Category: adenylosuccinate synthetase]] |
| - | [[Category: | + | [[Category: adss]] |
| - | [[Category: | + | [[Category: gtp]] |
| - | [[Category: | + | [[Category: hadacidin]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:14:58 2008'' |
Revision as of 00:14, 31 March 2008
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| , resolution 2.0Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Gene: | purA, adeK (Escherichia coli) | ||||||
| Activity: | Adenylosuccinate synthase, with EC number 6.3.4.4 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Fully ligated E.Coli Adenylosuccinate Synthetase with GTP, 2'-deoxy-IMP and Hadacidin
Overview
Adenylosuccinate synthetase catalyzes the first committed step in the de novo biosynthesis of AMP, coupling L-aspartate and IMP to form adenylosuccinate. Km values of IMP and 2'-deoxy-IMP are nearly identical with each substrate supporting comparable maximal velocities. Nonetheless, the Km value for L-aspartate and the Ki value for hadacidin (a competitive inhibitor with respect to L-aspartate) are 29-57-fold lower in the presence of IMP than in the presence of 2'-deoxy-IMP. Crystal structures of the synthetase ligated with hadacidin, GDP, and either 6-phosphoryl-IMP or 2'-deoxy-6-phosphoryl-IMP are identical except for the presence of a cavity normally occupied by the 2'-hydroxyl group of IMP. In the presence of 6-phosphoryl-IMP and GDP (hadacidin absent), the L-aspartate pocket can retain its fully ligated conformation, forming hydrogen bonds between the 2'-hydroxyl group of IMP and sequence-invariant residues. In the presence of 2'-deoxy-6-phosphoryl-IMP and GDP, however, the L-aspartate pocket is poorly ordered. The absence of the 2'-hydroxyl group of the deoxyribonucleotide may destabilize binding of the ligand to the L-aspartate pocket by disrupting hydrogen bonds that maintain a favorable protein conformation and by the introduction of a cavity into the fully ligated active site. At an approximate energy cost of 2.2 kcal/mol, the unfavorable thermodynamics of cavity formation may be the major factor in destabilizing ligands at the L-aspartate pocket.
About this Structure
2GCQ is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Cavitation as a mechanism of substrate discrimination by adenylosuccinate synthetases., Iancu CV, Zhou Y, Borza T, Fromm HJ, Honzatko RB, Biochemistry. 2006 Sep 26;45(38):11703-11. PMID:16981730
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