1y3i

From Proteopedia

(Difference between revisions)

Revision as of 10:32, 6 January 2021

Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex

Structural highlights

1y3i is a 2 chain structure with sequence from "bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1y3h
Gene:	pPnk ("Bacillus tuberculosis" (Zopf 1883) Klein 1884)
Activity:	NAD(+) kinase, with EC number 2.7.1.23
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[NADK_MYCTU] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. It can use ATP and other nucleoside triphosphates as well as inorganic polyphosphate (poly(P)) as a source of phosphorus.[HAMAP-Rule:MF_00361]^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

NAD kinase is a key enzyme in NADP biosynthesis. We solved the crystal structure of polyphosphate/ATP-NAD kinase from Mycobacterium tuberculosis (Ppnk) complexed with NAD (Ppnk-NAD) at 2.6A resolution using apo-Ppnk structure solved in this work, and revealed the details of the structure and NAD-binding site. Superimposition of tertiary structures of apo-Ppnk and Ppnk-NAD demonstrated a substantial conformational difference in a loop (Ppnk-flexible loop). As a quaternary structure, these Ppnk structures exhibited tetramer as in solution condition. Notably, the Ppnk-flexible loop was involved in the intersubunit contact and probably related to the NAD-binding of the other subunit. Furthermore, the two residues (Asp189, His226) substantially contributed to creating NAD-binding site on the other subunit. The two residues and the residues involved in NAD-binding were conserved. However, residues corresponding to the Ppnk-flexible loop were not conserved, making us to speculate that the Ppnk-flexible loop may be Ppnk-specific.

NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex.,Mori S, Yamasaki M, Maruyama Y, Momma K, Kawai S, Hashimoto W, Mikami B, Murata K Biochem Biophys Res Commun. 2005 Feb 11;327(2):500-8. PMID:15629142^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kawai S, Mori S, Mukai T, Suzuki S, Yamada T, Hashimoto W, Murata K. Inorganic Polyphosphate/ATP-NAD kinase of Micrococcus flavus and Mycobacterium tuberculosis H37Rv. Biochem Biophys Res Commun. 2000 Sep 16;276(1):57-63. PMID:11006082 doi:http://dx.doi.org/10.1006/bbrc.2000.3433
↑ Raffaelli N, Finaurini L, Mazzola F, Pucci L, Sorci L, Amici A, Magni G. Characterization of Mycobacterium tuberculosis NAD kinase: functional analysis of the full-length enzyme by site-directed mutagenesis. Biochemistry. 2004 Jun 15;43(23):7610-7. PMID:15182203 doi:http://dx.doi.org/10.1021/bi049650w
↑ Mori S, Yamasaki M, Maruyama Y, Momma K, Kawai S, Hashimoto W, Mikami B, Murata K. NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex. Biochem Biophys Res Commun. 2005 Feb 11;327(2):500-8. PMID:15629142 doi:10.1016/j.bbrc.2004.11.163

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1y3i"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex==
-<StructureSection load='1y3i' size='340' side='right' caption='[[1y3i]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='1y3i' size='340' side='right'caption='[[1y3i]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1y3i]] is a 2 chain structure with sequence from [http://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=1Y3I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1y3i]] is a 2 chain structure with sequence from [http://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=1Y3I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Y3I FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1y3h|1y3h]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1y3h|1y3h]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pPnk ([http://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'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3i OCA], [http://pdbe.org/1y3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y3i RCSB], [http://www.ebi.ac.uk/pdbsum/1y3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3i ProSAT], [http://www.topsan.org/Proteins/TBSGC/1y3i TOPSAN]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1y3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3i OCA], [http://pdbe.org/1y3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y3i RCSB], [http://www.ebi.ac.uk/pdbsum/1y3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3i ProSAT], [http://www.topsan.org/Proteins/TBSGC/1y3i TOPSAN]</span></td></tr>
 </table>
 == Function ==
@@ Line 38: / Line 38: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Hashimoto, W]]
 [[Category: Kawai, S]]

1y3i

From Proteopedia

Revision as of 10:32, 6 January 2021

Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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