This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1odv

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Photoactive yellow protein 1-25 deletion mutant

Structural highlights

1odv is a 2 chain structure with sequence from Halorhodospira halophila. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.14Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYP_HALHA Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.

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

PAS (PER-ARNT-SIM) domains are a family of sensor protein domains involved in signal transduction in a wide range of organisms. Recent structural studies have revealed that these domains contain a structurally conserved alpha/beta-fold, whereas almost no conservation is observed at the amino acid sequence level. The photoactive yellow protein, a bacterial light sensor, has been proposed as the PAS structural prototype yet contains an N-terminal helix-turn-helix motif not found in other PAS domains. Here we describe the atomic resolution structure of a photoactive yellow protein deletion mutant lacking this motif, revealing that the PAS domain is indeed able to fold independently and is not affected by the removal of these residues. Computer simulations of currently known PAS domain structures reveal that these domains are not only structurally conserved but are also similar in their conformational flexibilities. The observed motions point to a possible common mechanism for communicating ligand binding/activation to downstream transducer proteins.

PAS domains. Common structure and common flexibility.,Vreede J, van der Horst MA, Hellingwerf KJ, Crielaard W, van Aalten DM J Biol Chem. 2003 May 16;278(20):18434-9. Epub 2003 Mar 14. PMID:12639952^[1]

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

References

↑ Vreede J, van der Horst MA, Hellingwerf KJ, Crielaard W, van Aalten DM. PAS domains. Common structure and common flexibility. J Biol Chem. 2003 May 16;278(20):18434-9. Epub 2003 Mar 14. PMID:12639952 doi:10.1074/jbc.M301701200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1odv"

@@ Line 3: / Line 3: @@
 <StructureSection load='1odv' size='340' side='right'caption='[[1odv]], [[Resolution|resolution]] 1.14&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1odv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_244 Dsm 244]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ODV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1odv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ODV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</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]] 1.14&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1d7e|1d7e]], [[1f98|1f98]], [[1f9i|1f9i]], [[1gsv|1gsv]], [[1gsw|1gsw]], [[1gsx|1gsx]], [[1kou|1kou]], [[1nwz|1nwz]], [[2phy|2phy]], [[2pyp|2pyp]], [[2pyr|2pyr]], [[3phy|3phy]], [[3pyp|3pyp]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></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=1odv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1odv OCA], [http://pdbe.org/1odv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1odv RCSB], [http://www.ebi.ac.uk/pdbsum/1odv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1odv 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=1odv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1odv OCA], [https://pdbe.org/1odv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1odv RCSB], [https://www.ebi.ac.uk/pdbsum/1odv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1odv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
+[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Dsm 244]]
+[[Category: Halorhodospira halophila]]
 [[Category: Large Structures]]
-[[Category: Aalten, D M.F Van]]
+[[Category: Crielaard W]]
-[[Category: Crielaard, W]]
+[[Category: Hellingwerf KJ]]
-[[Category: Hellingwerf, K J]]
+[[Category: Van Aalten DMF]]
-[[Category: Vreede, J]]
+[[Category: Van Der horst MA]]
-[[Category: Horst, M A.Van Der]]
+[[Category: Vreede J]]
-[[Category: P-coumaric acid]]
-[[Category: Photoactivity]]
-[[Category: Signalling]]

1odv

From Proteopedia

Current revision

Photoactive yellow protein 1-25 deletion mutant

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox