1kqp: Difference between revisions

Revision as of 23:03, 2 May 2008

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 Page seeded by OCA on Fri May 2 23:03:33 2008

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OCA

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 [[Image:1kqp.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1kqp |SIZE=350|CAPTION= <scene name='initialview01'>1kqp</scene>, resolution 1.03&Aring;
+The line below this paragraph, containing "STRUCTURE_1kqp", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|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>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|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>
+or leave the SCENE parameter empty for the default display.
-|GENE= OutB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
+-->
-|DOMAIN=
+{{STRUCTURE_1kqp|  PDB=1kqp  |  SCENE=  }}
-|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>
-}}
 '''NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION'''
@@ Line 24: / Line 21: @@
 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:[http://www.ncbi.nlm.nih.gov/pubmed/12077433 12077433]
 [[Category: Bacillus subtilis]]
-[[Category: NAD(+) synthase (glutamine-hydrolyzing)]]
 [[Category: Single protein]]
 [[Category: Brouillette, C.]]
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 [[Category: Moore, K.]]
 [[Category: Symersky, J.]]
-[[Category: amidotransferase]]
+[[Category: Amidotransferase]]
-[[Category: atp pyrophosphatase]]
+[[Category: Atp pyrophosphatase]]
-[[Category: ligase]]
+[[Category: Ligase]]
-[[Category: nad-adenylate]]
+[[Category: Nad-adenylate]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 23:03:33 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:52:14 2008''