Proteopedia

1ql0: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1ql0.jpg|left|200px]]


{{Structure
==Sm Endonuclease from Seratia marcenscens at atomic resolution==
|PDB= 1ql0 |SIZE=350|CAPTION= <scene name='initialview01'>1ql0</scene>, resolution 1.1&Aring;
<StructureSection load='1ql0' size='340' side='right'caption='[[1ql0]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
<table><tr><td colspan='2'>[[1ql0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QL0 FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Serratia_marcescens_nuclease Serratia marcescens nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.30.2 3.1.30.2]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1ql0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ql0 OCA], [https://pdbe.org/1ql0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ql0 RCSB], [https://www.ebi.ac.uk/pdbsum/1ql0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ql0 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NUCA_SERMA NUCA_SERMA] Catalyzes the hydrolysis of both DNA and RNA, double- or single-stranded, at the 3'position of the phosphodiester bond to produce 5'-phosphorylated mono-, di-, tri- and tetranucleotides. DNA is a slightly better substrate than RNA.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ql/1ql0_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1ql0 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional crystal structure of Serratia marcescens endonuclease has been refined at 1.1 A resolution to an R factor of 12.9% and an R(free) of 15.6% with the use of anisotropic temperature factors. The model contains 3694 non-H atoms, 715 water molecules, four sulfate ions and two Mg(2+)-binding sites at the active sites of the homodimeric protein. It is shown that the magnesium ion linked to the active-site Asn119 of each monomer is surrounded by five water molecules and shows an octahedral coordination geometry. The temperature factors for the bound Mg(2+) ions in the A and B subunits are 7.08 and 4.60 A(2), respectively, and the average temperature factors for the surrounding water molecules are 12.13 and 10.3 A(2), respectively. In comparison with earlier structures, alternative side-chain conformations are defined for 51 residues of the dimer, including the essential active-site residue Arg57. A plausible mechanism of enzyme function is proposed based on the high-resolution S. marcescens nuclease structure, the functional characteristics of the natural and mutational forms of the enzyme and consideration of its structural analogy with homing endo-nuclease I-PpoI.


'''SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT ATOMIC RESOLUTION'''
Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism.,Shlyapnikov SV, Lunin VV, Perbandt M, Polyakov KM, Lunin VY, Levdikov VM, Betzel C, Mikhailov AM Acta Crystallogr D Biol Crystallogr. 2000 May;56(Pt 5):567-72. PMID:10771425<ref>PMID:10771425</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ql0" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The three-dimensional crystal structure of Serratia marcescens endonuclease has been refined at 1.1 A resolution to an R factor of 12.9% and an R(free) of 15.6% with the use of anisotropic temperature factors. The model contains 3694 non-H atoms, 715 water molecules, four sulfate ions and two Mg(2+)-binding sites at the active sites of the homodimeric protein. It is shown that the magnesium ion linked to the active-site Asn119 of each monomer is surrounded by five water molecules and shows an octahedral coordination geometry. The temperature factors for the bound Mg(2+) ions in the A and B subunits are 7.08 and 4.60 A(2), respectively, and the average temperature factors for the surrounding water molecules are 12.13 and 10.3 A(2), respectively. In comparison with earlier structures, alternative side-chain conformations are defined for 51 residues of the dimer, including the essential active-site residue Arg57. A plausible mechanism of enzyme function is proposed based on the high-resolution S. marcescens nuclease structure, the functional characteristics of the natural and mutational forms of the enzyme and consideration of its structural analogy with homing endo-nuclease I-PpoI.
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 
== References ==
==About this Structure==
<references/>
1QL0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QL0 OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism., Shlyapnikov SV, Lunin VV, Perbandt M, Polyakov KM, Lunin VY, Levdikov VM, Betzel C, Mikhailov AM, Acta Crystallogr D Biol Crystallogr. 2000 May;56(Pt 5):567-72. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10771425 10771425]
[[Category: Serratia marcescens]]
[[Category: Serratia marcescens]]
[[Category: Serratia marcescens nuclease]]
[[Category: Betzel CH]]
[[Category: Single protein]]
[[Category: Mikhailov AM]]
[[Category: Betzel, C H.]]
[[Category: Perbandt M]]
[[Category: Mikhailov, A M.]]
[[Category: Perbandt, M.]]
[[Category: MG]]
[[Category: endonuclease]]
[[Category: hydrolase]]
[[Category: magnesium]]
[[Category: nuclease]]
[[Category: signal]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:39:04 2008''

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/w/1ql0"