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| | <StructureSection load='2vu5' size='340' side='right'caption='[[2vu5]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='2vu5' size='340' side='right'caption='[[2vu5]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2vu5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VU5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VU5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2vu5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VU5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VU5 FirstGlance]. <br> |
| - | </td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></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]] 2Å</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=2vu5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vu5 OCA], [https://pdbe.org/2vu5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vu5 RCSB], [https://www.ebi.ac.uk/pdbsum/2vu5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vu5 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=2vu5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vu5 OCA], [https://pdbe.org/2vu5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vu5 RCSB], [https://www.ebi.ac.uk/pdbsum/2vu5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vu5 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NDK_BACAN NDK_BACAN]] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity).
| + | [https://www.uniprot.org/uniprot/NDK_BACAN NDK_BACAN] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Large Structures]] | |
| - | [[Category: Nucleoside-diphosphate kinase]] | |
| - | [[Category: Aggarwal, A]] | |
| - | [[Category: Dube, D]] | |
| - | [[Category: Misra, G]] | |
| - | [[Category: Ramachandran, R]] | |
| - | [[Category: Singh, Y]] | |
| - | [[Category: Zaman, M S]] | |
| - | [[Category: Atp-binding]] | |
| | [[Category: Bacillus anthracis]] | | [[Category: Bacillus anthracis]] |
| - | [[Category: Cytoplasm]] | + | [[Category: Large Structures]] |
| - | [[Category: Kinase]] | + | [[Category: Aggarwal A]] |
| - | [[Category: Magnesium]] | + | [[Category: Dube D]] |
| - | [[Category: Metal-binding]] | + | [[Category: Misra G]] |
| - | [[Category: Nucleoside diphosphate kinase]] | + | [[Category: Ramachandran R]] |
| - | [[Category: Nucleotide metabolism]] | + | [[Category: Singh Y]] |
| - | [[Category: Nucleotide-binding]] | + | [[Category: Zaman MS]] |
| - | [[Category: Phosphoprotein]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
NDK_BACAN Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity).
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
Nucleoside diphosphate kinases (Ndks) play an important role in a plethora of regulatory and metabolic functions. Inhibition of the B. anthracis Ndk mRNA results in the formation of nonviable aberrant spores. We report the characterization and crystal structure of the enzyme from B. anthracis nucleoside diphosphate kinase (BaNdk), the first from sporulating bacteria. The enzyme, although from a mesophilic source, is active at extremes of pH (3.5-10.5), temperature (10-95 degrees C) and ionic strength (0.25-4.0M NaCl). It exists as a hexamer that is composed of two SDS-stable trimers interacting in a back-to-back association; mutational analysis confirms that the enzyme is a histidine kinase. The high-resolution crystal structure reported here reveals an unanticipated change in the conformation of residues between 43 and 63 that also regulates substrate entry in other Ndks. A comparative structural analysis involving Ndks from seven mesophiles and three thermophiles has resulted in the delineation of the structure into relatively rigid and flexible regions. The analysis suggests that the larger number of intramolecular hydrogen bonds and to a lesser extent ionic interactions in BaNdk contributes to its high thermostability. Mutational analysis and Molecular Dynamics simulations were used to probe the role of a highly conserved Gly19 (present at the oligomeric interface in most of the Ndks). The results suggest that the mutation leads to a rigidification of those residues that facilitate substrate entry and consequently leads to a large reduction in the kinase activity. Overall, the enzyme characterization helps to understand its apparent adaptation to perform under stress conditions. Proteins 2009. (c) 2009 Wiley-Liss, Inc.
Crystal structure of the Bacillus anthracis nucleoside diphosphate kinase and its characterization reveals an enzyme adapted to perform under stress conditions.,Misra G, Aggarwal A, Dube D, Zaman MS, Singh Y, Ramachandran R Proteins. 2009 Jan 14. PMID:19241473[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Misra G, Aggarwal A, Dube D, Zaman MS, Singh Y, Ramachandran R. Crystal structure of the Bacillus anthracis nucleoside diphosphate kinase and its characterization reveals an enzyme adapted to perform under stress conditions. Proteins. 2009 Jan 14. PMID:19241473 doi:10.1002/prot.22364
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