4wuc

From Proteopedia

(Difference between revisions)

Current revision

N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM NaCl condition

Structural highlights

4wuc is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GYRB_ECOLI DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K(+), is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K(+) ion that interacts directly with the alpha-phosphate of ATP, and site 2, which preferentially binds an Na(+) ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites.

The role of monovalent cations in the ATPase reaction of DNA gyrase.,Hearnshaw SJ, Chung TT, Stevenson CE, Maxwell A, Lawson DM Acta Crystallogr D Biol Crystallogr. 2015 Apr;71(Pt 4):996-1005. doi:, 10.1107/S1399004715002916. Epub 2015 Mar 27. PMID:25849408^[4]

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

References

↑ Noble CG, Maxwell A. The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. J Mol Biol. 2002 Apr 26;318(2):361-71. PMID:12051843 doi:http://dx.doi.org/10.1016/S0022-2836(02)00049-9
↑ Sissi C, Chemello A, Vazquez E, Mitchenall LA, Maxwell A, Palumbo M. DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action. Biochemistry. 2008 Aug 19;47(33):8538-45. doi: 10.1021/bi800480j. Epub 2008 Jul, 22. PMID:18642932 doi:http://dx.doi.org/10.1021/bi800480j
↑ Schoeffler AJ, May AP, Berger JM. A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Res. 2010 Jul 31. PMID:20675723 doi:10.1093/nar/gkq665
↑ Hearnshaw SJ, Chung TT, Stevenson CE, Maxwell A, Lawson DM. The role of monovalent cations in the ATPase reaction of DNA gyrase. Acta Crystallogr D Biol Crystallogr. 2015 Apr;71(Pt 4):996-1005. doi:, 10.1107/S1399004715002916. Epub 2015 Mar 27. PMID:25849408 doi:http://dx.doi.org/10.1107/S1399004715002916

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4wuc"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4wuc is ON HOLD  until Paper Publication
+==N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM NaCl condition==
+<StructureSection load='4wuc' size='340' side='right'caption='[[4wuc]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4wuc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WUC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WUC FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4wuc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wuc OCA], [https://pdbe.org/4wuc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wuc RCSB], [https://www.ebi.ac.uk/pdbsum/4wuc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wuc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GYRB_ECOLI GYRB_ECOLI] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.<ref>PMID:12051843</ref> <ref>PMID:18642932</ref> <ref>PMID:20675723</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K(+), is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K(+) ion that interacts directly with the alpha-phosphate of ATP, and site 2, which preferentially binds an Na(+) ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites.
-Authors: Hearnshaw, S.J., Chung, T.T., Stevenson, C.E.M., Maxwell, A., Lawson, D.M.
+The role of monovalent cations in the ATPase reaction of DNA gyrase.,Hearnshaw SJ, Chung TT, Stevenson CE, Maxwell A, Lawson DM Acta Crystallogr D Biol Crystallogr. 2015 Apr;71(Pt 4):996-1005. doi:, 10.1107/S1399004715002916. Epub 2015 Mar 27. PMID:25849408<ref>PMID:25849408</ref>
-Description: N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM NaCl condition
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Chung, T.T]]
+<div class="pdbe-citations 4wuc" style="background-color:#fffaf0;"></div>
-[[Category: Stevenson, C.E.M]]
-[[Category: Hearnshaw, S.J]]
+==See Also==
-[[Category: Maxwell, A]]
+*[[Gyrase 3D Structures|Gyrase 3D Structures]]
-[[Category: Lawson, D.M]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Chung TT]]
+[[Category: Hearnshaw SJ]]
+[[Category: Lawson DM]]
+[[Category: Maxwell A]]
+[[Category: Stevenson CEM]]

4wuc

From Proteopedia

Current revision

N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM NaCl condition

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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