1ifx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:33, 16 August 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1ifx.png|left|200px]]
 
-
<!--
+
==CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH TWO MOLECULES DEAMIDO-NAD==
-
The line below this paragraph, containing "STRUCTURE_1ifx", creates the "Structure Box" on the page.
+
<StructureSection load='1ifx' size='340' side='right'caption='[[1ifx]], [[Resolution|resolution]] 2.25&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'>[[1ifx]] 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=1IFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IFX 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]] 2.25&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DND:NICOTINIC+ACID+ADENINE+DINUCLEOTIDE'>DND</scene></td></tr>
-
{{STRUCTURE_1ifx| PDB=1ifx | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ifx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifx OCA], [https://pdbe.org/1ifx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ifx RCSB], [https://www.ebi.ac.uk/pdbsum/1ifx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ifx 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/if/1ifx_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=1ifx 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+).
-
===CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH TWO MOLECULES DEAMIDO-NAD===
+
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>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1ifx" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_11375500}}, adds the Publication Abstract to the page
+
*[[NAD synthase|NAD synthase]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 11375500 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_11375500}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
1IFX 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=1IFX OCA].
+
-
 
+
-
==Reference==
+
-
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]
+
[[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: 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: Amidotransferase]]
+
-
[[Category: Atp]]
+
-
[[Category: Lyase]]
+
-
[[Category: Nh3 dependent]]
+
-
[[Category: Pyrophosphatase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 10:54:51 2008''
+

Current revision

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH TWO MOLECULES DEAMIDO-NAD

PDB ID 1ifx

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/1ifx"
Personal tools