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3k9z

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Revision as of 19:25, 5 August 2016

Rational Design of a Structural and Functional Nitric Oxide Reductase

Structural highlights

3k9z is a 1 chain structure with sequence from Phycd. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	swMB (PHYCD)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.

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

Protein design provides a rigorous test of our knowledge about proteins and allows the creation of novel enzymes for biotechnological applications. Whereas progress has been made in designing proteins that mimic native proteins structurally, it is more difficult to design functional proteins. In comparison to recent successes in designing non-metalloproteins, it is even more challenging to rationally design metalloproteins that reproduce both the structure and function of native metalloenzymes. This is because protein metal-binding sites are much more varied than non-metal-containing sites, in terms of different metal ion oxidation states, preferred geometry and metal ion ligand donor sets. Because of their variability, it has been difficult to predict metal-binding site properties in silico, as many of the parameters, such as force fields, are ill-defined. Therefore, the successful design of a structural and functional metalloprotein would greatly advance the field of protein design and our understanding of enzymes. Here we report a successful, rational design of a structural and functional model of a metalloprotein, nitric oxide reductase (NOR), by introducing three histidines and one glutamate, predicted as ligands in the active site of NOR, into the distal pocket of myoglobin. A crystal structure of the designed protein confirms that the minimized computer model contains a haem/non-haem Fe(B) centre that is remarkably similar to that in the crystal structure. This designed protein also exhibits NO reduction activity, and so models both the structure and function of NOR, offering insight that the active site glutamate is required for both iron binding and activity. These results show that structural and functional metalloproteins can be rationally designed in silico.

Rational design of a structural and functional nitric oxide reductase.,Yeung N, Lin YW, Gao YG, Zhao X, Russell BS, Lei L, Miner KD, Robinson H, Lu Y Nature. 2009 Dec 24;462(7276):1079-82. Epub 2009 Nov 25. PMID:19940850^[1]

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

References

↑ Yeung N, Lin YW, Gao YG, Zhao X, Russell BS, Lei L, Miner KD, Robinson H, Lu Y. Rational design of a structural and functional nitric oxide reductase. Nature. 2009 Dec 24;462(7276):1079-82. Epub 2009 Nov 25. PMID:19940850 doi:10.1038/nature08620

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3k9z"

@@ Line 1: / Line 1: @@
 ==Rational Design of a Structural and Functional Nitric Oxide Reductase==
 <StructureSection load='3k9z' size='340' side='right' caption='[[3k9z]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3k9z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K9Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3k9z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phycd Phycd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K9Z FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">swMB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9755 Physeter catodon])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">swMB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9755 PHYCD])</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=3k9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k9z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k9z RCSB], [http://www.ebi.ac.uk/pdbsum/3k9z 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=3k9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k9z OCA], [http://pdbe.org/3k9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k9z RCSB], [http://www.ebi.ac.uk/pdbsum/3k9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k9z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MYG_PHYCA MYG_PHYCA]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
+[[http://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 18: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3k9z ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3k9z" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Physeter catodon]]
+[[Category: Phycd]]
 [[Category: Gao, Y G]]
 [[Category: Lei, L]]

3k9z

From Proteopedia

Revision as of 19:25, 5 August 2016

Rational Design of a Structural and Functional Nitric Oxide Reductase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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