2d0s

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the Cytochrome C552 from moderate thermophilic bacterium, hydrogenophilus thermoluteolus

Structural highlights

2d0s is a 1 chain structure with sequence from Hydrogenophilus thermoluteolus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q76IQ6_HYDTE

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

We have studied the structure-thermostability relationship using cytochromes c from mesophilic and thermophilic bacteria; Pseudomonas aeruginosa (PAc(551)) growing at 37 degrees C and Hydrogenobacter thermophilus (HTc(552)) at 72 degrees C and showed that only five residues primarily differentiate their stabilities. For a more comprehensive study, we found Hydrogenophilus thermoluteolus (Pseudomonas hydrogenothermophila) growing at 52 degrees C and showed the moderate stability of the cytochrome c from this bacterium (PHc(552)). To explore the stabilization mechanisms, the crystal structure of PHc(552) was determined by X-ray analysis. The solution structure of HTc(552) elucidated previously by NMR was refined using distributed computational implementation. Furthermore, the recently reported crystal structure of HTc(552) has become available [Travaglini-Allocatelli, C. et al. (2005) J. Biol. Chem. 280, 25729-25734]. When the structures of these three cytochromes c were combined, this revealed that the five residues, corresponding to those mentioned above, determine the difference of stabilities among them as well. These facts suggested the stabilization mechanisms as follows: (1) improved van der Waals interactions by packing optimization at the N-terminal helix, (2) attractive electrostatic interactions with the heme propionate group, and (3) favorable van der Waals interaction with the heme. This comparative study, by supplementing the structural information of PHc(552) with its complementary feature, demonstrates that just a small number of amino acid residues determine the overall molecular stability by means of additivity of the effects of their substitutions. It is interesting that, in naturally occurring proteins, these adaptation strategies are accommodated by these bacteria to survive in the wide range of thermal conditions.

Structure of cytochrome c552 from a moderate thermophilic bacterium, Hydrogenophilus thermoluteolus: comparative study on the thermostability of cytochrome c.,Nakamura S, Ichiki S, Takashima H, Uchiyama S, Hasegawa J, Kobayashi Y, Sambongi Y, Ohkubo T Biochemistry. 2006 May 16;45(19):6115-23. PMID:16681384^[1]

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

References

↑ Nakamura S, Ichiki S, Takashima H, Uchiyama S, Hasegawa J, Kobayashi Y, Sambongi Y, Ohkubo T. Structure of cytochrome c552 from a moderate thermophilic bacterium, Hydrogenophilus thermoluteolus: comparative study on the thermostability of cytochrome c. Biochemistry. 2006 May 16;45(19):6115-23. PMID:16681384 doi:10.1021/bi0520131

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/2d0s"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the Cytochrome C552 from moderate thermophilic bacterium, hydrogenophilus thermoluteolus==
-<StructureSection load='2d0s' size='340' side='right' caption='[[2d0s]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='2d0s' size='340' side='right'caption='[[2d0s]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2d0s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_106958 Cip 106958]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D0S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2d0s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hydrogenophilus_thermoluteolus Hydrogenophilus thermoluteolus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</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]] 2.2&#8491;</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=2d0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0s OCA], [http://pdbe.org/2d0s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d0s RCSB], [http://www.ebi.ac.uk/pdbsum/2d0s PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></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=2d0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0s OCA], [https://pdbe.org/2d0s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0s RCSB], [https://www.ebi.ac.uk/pdbsum/2d0s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0s ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q76IQ6_HYDTE Q76IQ6_HYDTE]
 == 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/d0/2d0s_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/2d0s_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <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/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=2d0s ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 31: @@
 ==See Also==
-*[[Nitric reductase|Nitric reductase]]
+*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cip 106958]]
+[[Category: Hydrogenophilus thermoluteolus]]
-[[Category: Hasegawa, J]]
+[[Category: Large Structures]]
-[[Category: Ichiki, S I]]
+[[Category: Hasegawa J]]
-[[Category: Kobayashi, Y]]
+[[Category: Ichiki SI]]
-[[Category: Nakamura, S]]
+[[Category: Kobayashi Y]]
-[[Category: Ohkubo, T]]
+[[Category: Nakamura S]]
-[[Category: Sambongi, Y]]
+[[Category: Ohkubo T]]
-[[Category: Takashima, H]]
+[[Category: Sambongi Y]]
-[[Category: Uchiyama, S]]
+[[Category: Takashima H]]
-[[Category: Electron transport]]
+[[Category: Uchiyama S]]
-[[Category: Heme protein]]

2d0s

From Proteopedia

Current revision

Crystal structure of the Cytochrome C552 from moderate thermophilic bacterium, hydrogenophilus thermoluteolus

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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