1kqp: Difference between revisions
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|PDB= 1kqp |SIZE=350|CAPTION= <scene name='initialview01'>1kqp</scene>, resolution 1.03Å | |PDB= 1kqp |SIZE=350|CAPTION= <scene name='initialview01'>1kqp</scene>, resolution 1.03Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=ADJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE-ADENYLATE+INTERMEDIATE'>ADJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/NAD(+)_synthase_(glutamine-hydrolyzing) NAD(+) synthase (glutamine-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.1 6.3.5.1] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_synthase_(glutamine-hydrolyzing) NAD(+) synthase (glutamine-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.1 6.3.5.1] </span> | ||
|GENE= OutB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]) | |GENE= OutB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1nsy|1NSY]], [[2nsy|2NSY]], [[1ee1|1EE1]], [[1ifx|1IFX]], [[1fyd|1FYD]], [[1ih8|1IH8]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqp OCA], [http://www.ebi.ac.uk/pdbsum/1kqp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kqp RCSB]</span> | |||
}} | }} | ||
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[[Category: Moore, K.]] | [[Category: Moore, K.]] | ||
[[Category: Symersky, J.]] | [[Category: Symersky, J.]] | ||
[[Category: amidotransferase]] | [[Category: amidotransferase]] | ||
[[Category: atp pyrophosphatase]] | [[Category: atp pyrophosphatase]] | ||
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[[Category: nad-adenylate]] | [[Category: nad-adenylate]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:52:14 2008'' | ||
Revision as of 21:52, 30 March 2008
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| , resolution 1.03Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Gene: | OutB (Bacillus subtilis) | ||||||
| Activity: | NAD(+) synthase (glutamine-hydrolyzing), with EC number 6.3.5.1 | ||||||
| Related: | 1NSY, 2NSY, 1EE1, 1IFX, 1FYD, 1IH8
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION
OverviewOverview
The final step of NAD+ biosynthesis includes an amide transfer to nicotinic acid adenine dinucleotide (NaAD) catalyzed by NAD+ synthetase. This enzyme was co-crystallized in microgravity with natural substrates NaAD and ATP at pH 8.5. The crystal was exposed to ammonium ions, synchrotron diffraction data were collected and the atomic model was refined anisotropically at 1 A resolution to R = 11.63%. Both binding sites are occupied by the NAD-adenylate intermediate, pyrophosphate and two magnesium ions. The atomic resolution of the structure allows better definition of non-planar peptide groups, reveals a low mean anisotropy of protein and substrate atoms and indicates the H-atom positions of the phosphoester group of the reaction intermediate. The phosphoester group is protonated at the carbonyl O atom O7N, suggesting a carbenium-ion structure stabilized by interactions with two solvent sites presumably occupied by ammonia and a water molecule. A mechanism is proposed for the second catalytic step, which includes a nucleophilic attack by the ammonia molecule on the intermediate.
About this StructureAbout this Structure
1KQP is a Single protein structure of sequence from Bacillus subtilis. Full crystallographic information is available from OCA.
ReferenceReference
NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution., Symersky J, Devedjiev Y, Moore K, Brouillette C, DeLucas L, Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1138-46. Epub 2002, Jun 20. PMID:12077433
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