1nlk: Difference between revisions

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<StructureSection load='1nlk' size='340' side='right'caption='[[1nlk]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1nlk' size='340' side='right'caption='[[1nlk]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1nlk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_25232 Atcc 25232]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NLK FirstGlance]. <br>
<table><tr><td colspan='2'>[[1nlk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NLK FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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&#8491;</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>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1nlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nlk OCA], [https://pdbe.org/1nlk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nlk RCSB], [https://www.ebi.ac.uk/pdbsum/1nlk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nlk 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=1nlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nlk OCA], [https://pdbe.org/1nlk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nlk RCSB], [https://www.ebi.ac.uk/pdbsum/1nlk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nlk ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/NDK_MYXXA NDK_MYXXA]] Major role in the synthesis of nucleoside triphosphates other than ATP.[HAMAP-Rule:MF_00451]  
[https://www.uniprot.org/uniprot/NDK_MYXXA NDK_MYXXA] Major role in the synthesis of nucleoside triphosphates other than ATP.[HAMAP-Rule:MF_00451]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1nlk ConSurf].
</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=1nlk ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The X-ray crystallographic structure of nucleoside diphosphate (NDP) kinase from Myxococcus xanthus has been determined using multiple isomorphous replacement techniques and refined at 2.0 A resolution to a crystallographic R-factor of 0.17. This is the first report of the structure of an enzymatically active NDP kinase and of the enzyme with a bound nucleotide. The structure has been determined in P4(3)2(1)2 and I222 crystal forms. The enzyme monomer consists of a four-stranded antiparallel beta-sheet. The surfaces of the sheet are partially covered with five helical segments. There are two protein molecules in the asymmetric unit of the tetragonal crystal form. They form a dimer with an extensive interface in which 1092 A2 per monomer is buried. The majority of the contact area in the dimer interface is between hydrophobic or aromatic residues. Two dimers are related by a crystallographic 2-fold axis to yield a tetramer. This tetramer is also present in the orthorhombic crystals; however, in this case, the 222 symmetry is entirely crystallographic. Upon tetramer formation, an additional 473 A2 of solvent-accessible surface area from each monomer becomes buried. The interface between dimers in the tetramer is stabilized by salt bridges. Equilibrium sedimentation studies are consistent with the enzyme being a tetramer in solution. The structure of a complex of adenosine diphosphate (ADP) with the enzyme was determined and reveals that most of the nucleotide interactions with the protein are with the pyrophosphate and ribose groups, while the base has no hydrogen bonds with the protein and interacts only by stacking with the side chain of Phe59. The Mg2+ interacts with the pyrophosphate of the ADP and via a solvent molecule with the side chain of the conserved Asp120 residue. The mode of interaction with the nucleotide is novel, with the nucleotide binding at the side of the beta-sheet. The structures of the nucleotide in crystals grown in the presence or absence of Mg2+ are essentially identical. In addition, the phosphotransfer reaction from adenosine triphosphate (ATP) to the enzyme can occur without Mg2+. This suggests that only the second step of the reaction in which the enzyme transfers the phosphate to a nucleoside diphosphate acceptor is significantly catalyzed by the metal.
Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 A resolution.,Williams RL, Oren DA, Munoz-Dorado J, Inouye S, Inouye M, Arnold E J Mol Biol. 1993 Dec 20;234(4):1230-47. PMID:8263923<ref>PMID:8263923</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1nlk" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 25232]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Nucleoside-diphosphate kinase]]
[[Category: Myxococcus xanthus]]
[[Category: Williams, R L]]
[[Category: Williams RL]]

Latest revision as of 10:57, 14 February 2024

CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTIONCRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION

Structural highlights

1nlk is a 2 chain structure with sequence from Myxococcus xanthus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NDK_MYXXA Major role in the synthesis of nucleoside triphosphates other than ATP.[HAMAP-Rule:MF_00451]

Evolutionary Conservation

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

See Also

1nlk, resolution 2.00Å

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