3sdb: Difference between revisions

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<StructureSection load='3sdb' size='340' side='right'caption='[[3sdb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3sdb' size='340' side='right'caption='[[3sdb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3sdb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SDB FirstGlance]. <br>
<table><tr><td colspan='2'>[[3sdb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SDB FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dla|3dla]], [[3seq|3seq]], [[3sez|3sez]]</div></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.0017&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MT2513, MTCY428.08, nadE, Rv2438c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/NAD(+)_synthase_(glutamine-hydrolyzing) NAD(+) synthase (glutamine-hydrolyzing)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.1 6.3.5.1] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3sdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sdb OCA], [https://pdbe.org/3sdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sdb RCSB], [https://www.ebi.ac.uk/pdbsum/3sdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sdb ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3sdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sdb OCA], [https://pdbe.org/3sdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sdb RCSB], [https://www.ebi.ac.uk/pdbsum/3sdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sdb ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/NADE_MYCTU NADE_MYCTU]] Can use both glutamine or ammonia as a nitrogen source.  
[https://www.uniprot.org/uniprot/NADE_MYCTU NADE_MYCTU] Can use both glutamine or ammonia as a nitrogen source.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Glutamine-dependent NAD+ synthetase is an essential enzyme and a validated drug target in Mycobacterium tuberculosis (mtuNadE). It catalyses the ATP-dependent formation of NAD+ from NaAD+ (nicotinic acid-adenine dinucleotide) at the synthetase active site and glutamine hydrolysis at the glutaminase active site. An ammonia tunnel 40 A (1 A=0.1 nm) long allows transfer of ammonia from one active site to the other. The enzyme displays stringent kinetic synergism; however, its regulatory mechanism is unclear. In the present paper, we report the structures of the inactive glutaminase C176A variant in an apo form and in three synthetase-ligand complexes with substrates (NaAD+/ATP), substrate analogue {NaAD+/AMP-CPP (adenosine 5'-[alpha,beta-methylene]triphosphate)} and intermediate analogues (NaAD+/AMP/PPi), as well as the structure of wild-type mtuNadE in a product complex (NAD+/AMP/PPi/glutamate). This series of structures provides snapshots of the ammonia tunnel during the catalytic cycle supported also by kinetics and mutagenesis studies. Three major constriction sites are observed in the tunnel: (i) at the entrance near the glutaminase active site; (ii) in the middle of the tunnel; and (iii) at the end near the synthetase active site. Variation in the number and radius of the tunnel constrictions is apparent in the crystal structures and is related to ligand binding at the synthetase domain. These results provide new insight into the regulation of ammonia transport in the intermolecular tunnel of mtuNadE.
 
Regulation of the intersubunit ammonia tunnel in Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase.,Chuenchor W, Doukov TI, Resto M, Chang A, Gerratana B Biochem J. 2012 Apr 15;443(2):417-26. PMID:22280445<ref>PMID:22280445</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3sdb" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[NAD synthase|NAD synthase]]
*[[NAD synthase|NAD synthase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chuenchor, W]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Gerratana, B]]
[[Category: Chuenchor W]]
[[Category: Ammonia tunneling]]
[[Category: Gerratana B]]
[[Category: Atp binding]]
[[Category: Glutaminase]]
[[Category: Glutamine-amidotransferase]]
[[Category: Glutamine-dependent nad+ synthetase]]
[[Category: Ligase]]
[[Category: Nad]]
[[Category: Nucleotide binding]]

Latest revision as of 15:54, 14 March 2024

Crystal structure of C176A mutant of glutamine-dependent NAD+ synthetase from M. tuberculosis in apo formCrystal structure of C176A mutant of glutamine-dependent NAD+ synthetase from M. tuberculosis in apo form

Structural highlights

3sdb is a 1 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.0017Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NADE_MYCTU Can use both glutamine or ammonia as a nitrogen source.

See Also

3sdb, resolution 2.00Å

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OCA
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