2avf: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='2avf' size='340' side='right'caption='[[2avf]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='2avf' size='340' side='right'caption='[[2avf]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2avf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_cycloclastes"_(gray_and_thornton)_bergey_et_al. "achromobacter cycloclastes" (gray and thornton) bergey et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AVF FirstGlance]. <br>
<table><tr><td colspan='2'>[[2avf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AVF FirstGlance]. <br>
</td></tr><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=CU:COPPER+(II)+ION'>CU</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rzp|1rzp]], [[1rzq|1rzq]]</div></td></tr>
<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=CU:COPPER+(II)+ION'>CU</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [https://pdbe.org/2avf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [https://www.ebi.ac.uk/pdbsum/2avf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2avf ProSAT]</span></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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [https://pdbe.org/2avf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [https://www.ebi.ac.uk/pdbsum/2avf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2avf ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NIR_ACHCY NIR_ACHCY]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 19: Line 20:
</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=2avf 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=2avf ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Monoclinic crystal structure of C-terminal desundecapeptide nitrite reductase (NiRc-11) from Achromobacter cycloclastes was determined at 2.6A. NiRc-11 exists as a loose trimer in the crystal. Deletion of 11 residues eliminates all intersubunit hydrogen bonds mediated by the C-terminal tail. The rigid irregular coil 105-112, which constitutes part of the sidewall of the active site pocket, undergoes conformational changes and becomes highly flexible in NiRc-11. Correspondingly, the linker segments between the two copper sites 95-100 and 135-136 are partly relaxed in conformation, which leads to disrupted active site microenvironments responsible for the activity loss and spectral change of NiRc-11. Comparison with the native structure revealed a bulky residue Met331 fastened by hydrogen bonding, which may play a direct role in keeping the right copper site geometry by protruding its side chain against the irregular coil 105-112. Sequence alignment showed that the bulky residue is conserved at position 331, indicating an equal importance of C-terminal segment in other copper-containing nitrite reductases.
Crystal structure of C-terminal desundecapeptide nitrite reductase from Achromobacter cycloclastes.,Li HT, Chang T, Chang WC, Chen CJ, Liu MY, Gui LL, Zhang JP, An XM, Chang WR Biochem Biophys Res Commun. 2005 Dec 30;338(4):1935-42. Epub 2005 Nov 15. PMID:16293231<ref>PMID:16293231</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2avf" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Achromobacter cycloclastes]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: An, X M]]
[[Category: An XM]]
[[Category: Chang, T]]
[[Category: Chang T]]
[[Category: Chang, W C]]
[[Category: Chang WC]]
[[Category: Chang, W R]]
[[Category: Chang WR]]
[[Category: Chen, C J]]
[[Category: Chen CJ]]
[[Category: Gui, L L]]
[[Category: Gui LL]]
[[Category: Li, H T]]
[[Category: Li HT]]
[[Category: Liu, M Y]]
[[Category: Liu MY]]
[[Category: Zhang, J P]]
[[Category: Zhang JP]]
[[Category: Beta barrel trimer]]
[[Category: Oxidoreductase]]

Latest revision as of 16:42, 13 March 2024

Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastesCrystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes

Structural highlights

2avf is a 6 chain structure with sequence from Achromobacter cycloclastes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NIR_ACHCY

Evolutionary Conservation

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

See Also

2avf, resolution 2.60Å

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2avf&oldid=4088409"