This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1ih8

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:33, 16 August 2023) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ih8.gif|left|200px]]
 
-
<!--
+
==NH3-dependent NAD+ Synthetase from Bacillus subtilis Complexed with AMP-CPP and Mg2+ ions.==
-
The line below this paragraph, containing "STRUCTURE_1ih8", creates the "Structure Box" on the page.
+
<StructureSection load='1ih8' size='340' side='right'caption='[[1ih8]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1ih8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IH8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IH8 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
{{STRUCTURE_1ih8| PDB=1ih8 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ih8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ih8 OCA], [https://pdbe.org/1ih8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ih8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ih8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ih8 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/NADE_BACSU NADE_BACSU] Catalyzes a key step in NAD biosynthesis, transforming deamido-NAD into NAD by a two-step reaction.[HAMAP-Rule:MF_00193]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ih/1ih8_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ih8 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The NH(3)-dependent NAD(+) synthetase (NADS) participates in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) by transforming nicotinic acid adenine dinucleotide (NaAD) to NAD(+). The structural behavior of the active site, including stabilization of flexible loops 82-87 and 204-225, has been studied by determination of the crystal structures of complexes of NADS with natural substrates and a substrate analog. Both loops are stabilized independently of NaAD and solely from the ATP-binding site. Analysis of the binding contacts suggests that the minor loop 82-87 is stabilized primarily by a hydrogen bond with the adenine base of ATP. Formation of a coordination complex with Mg(2+) in the ATP-binding site may contribute to the stabilization of the major loop 204-225. The major loop has a role in substrate recognition and stabilization, in addition to the protection of the reaction intermediate described previously. A second and novel Mg(2+) position has been observed closer to the NaAD-binding site in the structure crystallized at pH 7.5, where the enzyme is active. This could therefore be the catalytically active Mg(2+).
-
'''NH3-dependent NAD+ Synthetase from Bacillus subtilis Complexed with AMP-CPP and Mg2+ ions.'''
+
Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis.,Devedjiev Y, Symersky J, Singh R, Jedrzejas M, Brouillette C, Brouillette W, Muccio D, Chattopadhyay D, DeLucas L Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):806-12. Epub 2001, May 25. PMID:11375500<ref>PMID:11375500</ref>
-
 
+
-
 
+
-
==Overview==
+
-
The NH(3)-dependent NAD(+) synthetase (NADS) participates in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) by transforming nicotinic acid adenine dinucleotide (NaAD) to NAD(+). The structural behavior of the active site, including stabilization of flexible loops 82-87 and 204-225, has been studied by determination of the crystal structures of complexes of NADS with natural substrates and a substrate analog. Both loops are stabilized independently of NaAD and solely from the ATP-binding site. Analysis of the binding contacts suggests that the minor loop 82-87 is stabilized primarily by a hydrogen bond with the adenine base of ATP. Formation of a coordination complex with Mg(2+) in the ATP-binding site may contribute to the stabilization of the major loop 204-225. The major loop has a role in substrate recognition and stabilization, in addition to the protection of the reaction intermediate described previously. A second and novel Mg(2+) position has been observed closer to the NaAD-binding site in the structure crystallized at pH 7.5, where the enzyme is active. This could therefore be the catalytically active Mg(2+).
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
1IH8 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=1IH8 OCA].
+
</div>
 +
<div class="pdbe-citations 1ih8" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis., Devedjiev Y, Symersky J, Singh R, Jedrzejas M, Brouillette C, Brouillette W, Muccio D, Chattopadhyay D, DeLucas L, Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):806-12. Epub 2001, May 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11375500 11375500]
+
*[[NAD synthase|NAD synthase]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Brouillette, C.]]
+
[[Category: Brouillette C]]
-
[[Category: Brouillette, W.]]
+
[[Category: Brouillette W]]
-
[[Category: Chattopadhyay, D.]]
+
[[Category: Chattopadhyay D]]
-
[[Category: DeLucas, L.]]
+
[[Category: DeLucas L]]
-
[[Category: Devedjiev, Y.]]
+
[[Category: Devedjiev Y]]
-
[[Category: Jedrzejas, M.]]
+
[[Category: Jedrzejas M]]
-
[[Category: Muccio, D.]]
+
[[Category: Muccio D]]
-
[[Category: Singh, R.]]
+
[[Category: Singh R]]
-
[[Category: Symersky, J.]]
+
[[Category: Symersky J]]
-
[[Category: Active-site loop]]
+
-
[[Category: Amidotransferase]]
+
-
[[Category: Atp pyrophosphatase]]
+
-
[[Category: Ligase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 19:59:47 2008''
+

Current revision

NH3-dependent NAD+ Synthetase from Bacillus subtilis Complexed with AMP-CPP and Mg2+ ions.

PDB ID 1ih8

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ih8"
Personal tools