2qdy: Difference between revisions

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{{Seed}}
[[Image:2qdy.png|left|200px]]


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==Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270==
The line below this paragraph, containing "STRUCTURE_2qdy", creates the "Structure Box" on the page.
<StructureSection load='2qdy' size='340' side='right'caption='[[2qdy]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2qdy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QDY FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IBN:2-METHYLPROPAN-1-AMINE'>IBN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
{{STRUCTURE_2qdy|  PDB=2qdy  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qdy OCA], [https://pdbe.org/2qdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qdy RCSB], [https://www.ebi.ac.uk/pdbsum/2qdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qdy ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NHAA_RHOER NHAA_RHOER] NHase catalyzes the hydration of various nitrile compounds to the corresponding amides. Industrial production of acrylamide is now being developed using some of the enzymes of this class.
== 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/qd/2qdy_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=2qdy ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of Fe-type nitrile hydratase from Rhodococcus erythropolis AJ270 was determined at 1.3A resolution. The two cysteine residues (alphaCys(112) and alphaCys(114)) equatorially coordinated to the ferric ion were post-translationally modified to cysteine sulfinic acids. A glutamine residue (alphaGln(90)) in the active center gave double conformations. Based on the interactions among the enzyme, substrate and water molecules, a new mechanism of biocatalysis of nitrile hydratase was proposed, in which the water molecule activated by the glutamine residue performed as the nucleophile to attack on the nitrile which was simultaneously interacted by another water molecule coordinated to the ferric ion.


===Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270===
High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism.,Song L, Wang M, Shi J, Xue Z, Wang MX, Qian S Biochem Biophys Res Commun. 2007 Oct 19;362(2):319-24. Epub 2007 Aug 14. PMID:17716629<ref>PMID:17716629</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2qdy" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17716629}}, adds the Publication Abstract to the page
*[[Nitrile hydratase|Nitrile hydratase]]
(as it appears on PubMed at http://www.pubmed.gov), where 17716629 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17716629}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2QDY is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QDY OCA].
 
==Reference==
High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism., Song L, Wang M, Shi J, Xue Z, Wang MX, Qian S, Biochem Biophys Res Commun. 2007 Oct 19;362(2):319-24. Epub 2007 Aug 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17716629 17716629]
[[Category: Nitrile hydratase]]
[[Category: Protein complex]]
[[Category: Rhodococcus erythropolis]]
[[Category: Rhodococcus erythropolis]]
[[Category: Qian, S.]]
[[Category: Qian S]]
[[Category: Shi, J.]]
[[Category: Shi J]]
[[Category: Song, L.]]
[[Category: Song L]]
[[Category: Wang, M X.]]
[[Category: Wang M-X]]
[[Category: Xue, Z.]]
[[Category: Xue Z]]
[[Category: Lyase]]
[[Category: Nitrile hydratase]]
[[Category: Post translation]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 21:31:58 2008''

Latest revision as of 11:32, 30 October 2024

Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270

Structural highlights

2qdy is a 2 chain structure with sequence from Rhodococcus erythropolis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.3Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NHAA_RHOER NHase catalyzes the hydration of various nitrile compounds to the corresponding amides. Industrial production of acrylamide is now being developed using some of the enzymes of this class.

Evolutionary Conservation

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

Publication Abstract from PubMed

The crystal structure of Fe-type nitrile hydratase from Rhodococcus erythropolis AJ270 was determined at 1.3A resolution. The two cysteine residues (alphaCys(112) and alphaCys(114)) equatorially coordinated to the ferric ion were post-translationally modified to cysteine sulfinic acids. A glutamine residue (alphaGln(90)) in the active center gave double conformations. Based on the interactions among the enzyme, substrate and water molecules, a new mechanism of biocatalysis of nitrile hydratase was proposed, in which the water molecule activated by the glutamine residue performed as the nucleophile to attack on the nitrile which was simultaneously interacted by another water molecule coordinated to the ferric ion.

High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism.,Song L, Wang M, Shi J, Xue Z, Wang MX, Qian S Biochem Biophys Res Commun. 2007 Oct 19;362(2):319-24. Epub 2007 Aug 14. PMID:17716629[1]

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

See Also

References

  1. ↑ Song L, Wang M, Shi J, Xue Z, Wang MX, Qian S. High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism. Biochem Biophys Res Commun. 2007 Oct 19;362(2):319-24. Epub 2007 Aug 14. PMID:17716629 doi:http://dx.doi.org/10.1016/j.bbrc.2007.07.184

2qdy, resolution 1.30Å

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