1kqp: Difference between revisions

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Revision as of 13:20, 20 March 2008

File:1kqp.gif

, resolution 1.03Å

Ligands:

, , and

Gene:

OutB (Bacillus subtilis)

Activity:

NAD(+) synthase (glutamine-hydrolyzing), with EC number 6.3.5.1

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

Page seeded by OCA on Thu Mar 20 12:20:56 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1kqp.gif|left|200px]]<br /><applet load="1kqp" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1kqp.gif|left|200px]]
-caption="1kqp, resolution 1.03&Aring;" />
-'''NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION'''<br />
+ {{Structure
+|PDB= 1kqp |SIZE=350|CAPTION= <scene name='initialview01'>1kqp</scene>, resolution 1.03&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ADJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE-ADENYLATE+INTERMEDIATE'>ADJ</scene> and <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]
+|GENE= OutB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
+}}
+'''NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-KQP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=EDO:'>EDO</scene>, <scene name='pdbligand=ADJ:'>ADJ</scene> and <scene name='pdbligand=POP:'>POP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQP OCA].
+KQP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQP OCA].
 ==Reference==
-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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12077433 12077433]
+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)]]
@@ Line 28: / Line 37: @@
 [[Category: nad-adenylate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:36:55 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:20:56 2008''