5cns

From Proteopedia

(Difference between revisions)

Revision as of 16:37, 15 November 2017

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to CDP and dATP at 2.97 Angstroms resolution

Structural highlights

5cns is a 8 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Related:	5cnt, 5cnu, 5cnv
Gene:	nrdA, dnaF, b2234, JW2228 (ECOLI), nrdB, ftsB, b2235, JW2229 (ECOLI)
Activity:	Ribonucleoside-diphosphate reductase, with EC number 1.17.4.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RIR1_ECOLI] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines. [RIR2_ECOLI] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.

Publication Abstract from PubMed

Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR 'reads' the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell.

Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.,Zimanyi CM, Chen PY, Kang G, Funk MA, Drennan CL Elife. 2016 Jan 12;5. pii: e07141. doi: 10.7554/eLife.07141. PMID:26754917^[1]

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

References

↑ Zimanyi CM, Chen PY, Kang G, Funk MA, Drennan CL. Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli. Elife. 2016 Jan 12;5. pii: e07141. doi: 10.7554/eLife.07141. PMID:26754917 doi:http://dx.doi.org/10.7554/eLife.07141

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5cns"

@@ Line 3: / Line 3: @@
 <StructureSection load='5cns' size='340' side='right' caption='[[5cns]], [[Resolution|resolution]] 2.98&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5cns]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CNS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5cns]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CNS FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=DAT:2-DEOXYADENOSINE-5-DIPHOSPHATE'>DAT</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5cnt|5cnt]], [[5cnu|5cnu]], [[5cnv|5cnv]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nrdA, dnaF, b2234, JW2228 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), nrdB, ftsB, b2235, JW2229 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=5cns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cns OCA], [http://pdbe.org/5cns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cns RCSB], [http://www.ebi.ac.uk/pdbsum/5cns PDBsum]</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=5cns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cns OCA], [http://pdbe.org/5cns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cns RCSB], [http://www.ebi.ac.uk/pdbsum/5cns PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cns ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 24: / Line 25: @@
 __TOC__
 </StructureSection>
+[[Category: Ecoli]]
 [[Category: Ribonucleoside-diphosphate reductase]]
 [[Category: Chen, P Y.T]]

5cns

From Proteopedia

Revision as of 16:37, 15 November 2017

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to CDP and dATP at 2.97 Angstroms resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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