2prq: Difference between revisions

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


<!--
==X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica==
The line below this paragraph, containing "STRUCTURE_2prq", creates the "Structure Box" on the page.
<StructureSection load='2prq' size='340' side='right'caption='[[2prq]], [[Resolution|resolution]] 2.15&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'>[[2prq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PRQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PRQ 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]] 2.15&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
{{STRUCTURE_2prq|  PDB=2prq  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2prq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2prq OCA], [https://pdbe.org/2prq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2prq RCSB], [https://www.ebi.ac.uk/pdbsum/2prq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2prq ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/AMPX_VIBPR AMPX_VIBPR]
== 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/pr/2prq_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2prq ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The X-ray crystal structure of the Co(II)-loaded form of the aminopeptidase from Aeromonas proteolytica ([CoCo(AAP)]) was solved to 2.2A resolution. [CoCo(AAP)] folds into an alpha/beta globular domain with a twisted beta-sheet hydrophobic core sandwiched between alpha-helices, identical to [ZnZn(AAP)]. Co(II) binding to AAP does not introduce any major conformational changes to the overall protein structure and the amino acid residues ligated to the dicobalt(II) cluster in [CoCo(AAP)] are the same as those in the native Zn(II)-loaded structure with only minor perturbations in bond lengths. The Co(II)-Co(II) distance is 3.3A. Tris(hydroxymethyl)aminomethane (Tris) coordinates to the dinuclear Co(II) active site of AAP with one of the Tris hydroxyl oxygen atoms (O4) forming a single oxygen atom bridge between the two Co(II) ions. This is the only Tris atom coordinated to the metals with Co1-O and Co2-O bonds distances of 2.2 and 1.9A, respectively. Each of the Co(II) ions resides in a distorted trigonal bipyramidal geometry. This important structure bridges the gap between previous structural and spectroscopic studies performed on AAP and is discussed in this context.


===X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica===
X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica.,Munih P, Moulin A, Stamper CC, Bennett B, Ringe D, Petsko GA, Holz RC J Inorg Biochem. 2007 Aug;101(8):1099-107. Epub 2007 Apr 11. PMID:17574677<ref>PMID:17574677</ref>


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


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17574677}}, adds the Publication Abstract to the page
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17574677 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17574677}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2PRQ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PRQ OCA].
 
==Reference==
<ref group="xtra">PMID:17574677</ref><references group="xtra"/>
[[Category: Bacterial leucyl aminopeptidase]]
[[Category: Vibrio proteolyticus]]
[[Category: Vibrio proteolyticus]]
[[Category: Bennet, B.]]
[[Category: Bennet B]]
[[Category: Holz, R C.]]
[[Category: Holz RC]]
[[Category: Moulin, A.]]
[[Category: Moulin A]]
[[Category: Munih, P.]]
[[Category: Munih P]]
[[Category: Petsko, G A.]]
[[Category: Petsko GA]]
[[Category: Ringe, D.]]
[[Category: Ringe D]]
[[Category: Stamper, C C.]]
[[Category: Stamper CC]]
[[Category: Aminohydrolase]]
[[Category: Cobalt]]
[[Category: Metalloprotease]]
[[Category: Peptidase]]
[[Category: Tri]]
[[Category: X-ray]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:29:33 2009''

Latest revision as of 14:07, 30 August 2023

X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolyticaX-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica

Structural highlights

2prq is a 1 chain structure with sequence from Vibrio proteolyticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.15Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMPX_VIBPR

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 X-ray crystal structure of the Co(II)-loaded form of the aminopeptidase from Aeromonas proteolytica ([CoCo(AAP)]) was solved to 2.2A resolution. [CoCo(AAP)] folds into an alpha/beta globular domain with a twisted beta-sheet hydrophobic core sandwiched between alpha-helices, identical to [ZnZn(AAP)]. Co(II) binding to AAP does not introduce any major conformational changes to the overall protein structure and the amino acid residues ligated to the dicobalt(II) cluster in [CoCo(AAP)] are the same as those in the native Zn(II)-loaded structure with only minor perturbations in bond lengths. The Co(II)-Co(II) distance is 3.3A. Tris(hydroxymethyl)aminomethane (Tris) coordinates to the dinuclear Co(II) active site of AAP with one of the Tris hydroxyl oxygen atoms (O4) forming a single oxygen atom bridge between the two Co(II) ions. This is the only Tris atom coordinated to the metals with Co1-O and Co2-O bonds distances of 2.2 and 1.9A, respectively. Each of the Co(II) ions resides in a distorted trigonal bipyramidal geometry. This important structure bridges the gap between previous structural and spectroscopic studies performed on AAP and is discussed in this context.

X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica.,Munih P, Moulin A, Stamper CC, Bennett B, Ringe D, Petsko GA, Holz RC J Inorg Biochem. 2007 Aug;101(8):1099-107. Epub 2007 Apr 11. PMID:17574677[1]

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

See Also

References

  1. ↑ Munih P, Moulin A, Stamper CC, Bennett B, Ringe D, Petsko GA, Holz RC. X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica. J Inorg Biochem. 2007 Aug;101(8):1099-107. Epub 2007 Apr 11. PMID:17574677 doi:10.1016/j.jinorgbio.2007.03.010

2prq, resolution 2.15Å

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