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1noy

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[[Image:1noy.gif|left|200px]]
 
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==DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX==
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The line below this paragraph, containing "STRUCTURE_1noy", creates the "Structure Box" on the page.
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<StructureSection load='1noy' size='340' side='right'caption='[[1noy]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1noy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NOY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NOY FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1noy| PDB=1noy | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1noy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1noy OCA], [https://pdbe.org/1noy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1noy RCSB], [https://www.ebi.ac.uk/pdbsum/1noy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1noy ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPOL_BPT4 DPOL_BPT4] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/no/1noy_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1noy ConSurf].
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<div style="clear:both"></div>
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'''DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX'''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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We report the crystal structure of an NH2-terminal 388-residue fragment of T4 DNA polymerase (protein N388) refined at 2.2 A resolution. This fragment contains both the 3'-5' exonuclease active site and part of the autologous mRNA binding site (J. D. Karam, personal communication). The structure of a complex between the apoprotein N388 and a substrate, p(dT)3, has been refined at 2.5 A resolution to a crystallographic R-factor of 18.7%. Two divalent metal ion cofactors, Zn(II) and Mn(II), have been located in crystals of protein N388 which had been soaked in solutions containing Zn(II), Mn(II), or both. The structure of the 3'-5' exonuclease domain of protein N388 closely resembles the corresponding region in the Klenow fragment despite minimal sequence identity. The side chains of four carboxylate residues that serve as ligands for the two metal ions required for catalysis are located in geometrically equivalent positions in both proteins with a rms deviation of 0.87 A. There are two main differences between the 3'-5' exonuclease active site regions of the two proteins: (I) the OH of Tyr-497 in the Klenow fragment interacts with the scissile phosphate in the active site whereas the OH of the equivalent tyrosine (Tyr-320) in protein N388 points away from the active center; (II) different residues form of the binding pocket for the 3'-terminal bases of the substrate. In the protein N388 complex the 3'-terminal base of p(dT)3 is rotated approximately 60 degrees relative to the position that the corresponding base occupies in the p(dT)3 complex with the Klenow fragment. Finally, a separate domain (residues 1-96) of protein N388 may be involved in mRNA binding that results in translational regulation of T4 DNA polymerase (Pavlov &amp; Karam, 1994).
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[[Category: Escherichia virus T4]]
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: Konigsberg WH]]
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1NOY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NOY OCA].
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[[Category: Lin TC]]
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[[Category: Steitz TA]]
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==Reference==
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[[Category: Wang J]]
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Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions., Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA, Biochemistry. 1996 Jun 25;35(25):8110-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8679562 8679562]
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[[Category: Yu P]]
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[[Category: Enterobacteria phage t4]]
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[[Category: Single protein]]
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[[Category: Konigsberg, W H.]]
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[[Category: Lin, T C.]]
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[[Category: Steitz, T A.]]
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[[Category: Wang, J.]]
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[[Category: Yu, P.]]
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[[Category: Dna-binding]]
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[[Category: Exonuclease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:47:58 2008''
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Current revision

DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX

PDB ID 1noy

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