1gim
From Proteopedia
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|PDB= 1gim |SIZE=350|CAPTION= <scene name='initialview01'>1gim</scene>, resolution 2.5Å | |PDB= 1gim |SIZE=350|CAPTION= <scene name='initialview01'>1gim</scene>, resolution 2.5Å | ||
|SITE= <scene name='pdbsite=ASP:These+Residues+Make+Up+The+Guanine+Nucleotide+Binding+Si+...'>ASP</scene>, <scene name='pdbsite=GNS:These+Residues+Make+Up+The+Guanine+Nucleotide+Binding+Si+...'>GNS</scene> and <scene name='pdbsite=IMP:These+Residues+Make+Up+The+Guanine+Nucleotide+Binding+Si+...'>IMP</scene> | |SITE= <scene name='pdbsite=ASP:These+Residues+Make+Up+The+Guanine+Nucleotide+Binding+Si+...'>ASP</scene>, <scene name='pdbsite=GNS:These+Residues+Make+Up+The+Guanine+Nucleotide+Binding+Si+...'>GNS</scene> and <scene name='pdbsite=IMP:These+Residues+Make+Up+The+Guanine+Nucleotide+Binding+Si+...'>IMP</scene> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=GDP:GUANOSINE-5'-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=HAD:(CARBOXYHYDROXYAMINO)ETHANOIC+ACID'>HAD</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gim OCA], [http://www.ebi.ac.uk/pdbsum/1gim PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1gim RCSB]</span> | ||
}} | }} | ||
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[[Category: Honzatko, R B.]] | [[Category: Honzatko, R B.]] | ||
[[Category: Poland, B W.]] | [[Category: Poland, B W.]] | ||
| - | [[Category: GDP]] | ||
| - | [[Category: HAD]] | ||
| - | [[Category: IMP]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: NO3]] | ||
[[Category: gtp-hydrolyzing enzyme]] | [[Category: gtp-hydrolyzing enzyme]] | ||
[[Category: ligase (synthetase)]] | [[Category: ligase (synthetase)]] | ||
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[[Category: x-ray crystallography]] | [[Category: x-ray crystallography]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:44:55 2008'' |
Revision as of 17:44, 30 March 2008
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| , resolution 2.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , and | ||||||
| Ligands: | , , , , | ||||||
| Activity: | Adenylosuccinate synthase, with EC number 6.3.4.4 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH GDP, IMP, HADACIDIN, NO3-, AND MG2+. DATA COLLECTED AT 100K (PH 6.5)
Overview
Crystal structures of adenylosuccinate synthetase from Esherichia coli complexed with Mg2+, IMP, GDP, NO3- and hadacidin at 298 and 100 K have been refined to R-factors of 0.188 and 0.206 against data to 2.8 A and 2.5 A resolution, respectively. Conformational changes of up to 9 A relative to the unligated enzyme occur in loops that bind to Mg2+, GDP, IMP and hadacidin. Mg2+ binds directly to GDP, NO3-, hadacidin and the protein, but is only five-coordinated. Asp13, which approaches, but does not occupy the sixth coordination site of Mg2+, hydrogen bonds to N1 of IMP. The nitrogen atom of NO3- is approximately 2.7 A from O6 of IMP, reflecting a strong electrostatic interaction between the electron-deficient nitrogen atom and the electron-rich O6. The spatial relationships between GDP, NO3- and Mg2+ suggest an interaction between the beta,gamma-bridging oxygen atom of GTP and Mg2+ in the enzyme-substrate complex. His41 hydrogen bonds to the beta-phosphate group of GDP and approaches bound NO3-. The aldehyde group of hadacidin coordinates to the Mg2+, while its carboxyl group interacts with backbone amide groups 299 to 303 and the side-chain of Arg303. The 5'-phosphate group of IMP interacts with Asn38, Thr129, Thr239 and Arg143 (from a monomer related by 2-fold symmetry). A mechanism is proposed for the two-step reaction governed by the synthetase, in which His41 and Asp13 are essential catalytic side-chains.
About this Structure
1GIM is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with GDP, IMP hadacidin, NO3-, and Mg2+., Poland BW, Fromm HJ, Honzatko RB, J Mol Biol. 1996 Dec 20;264(5):1013-27. PMID:9000627
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