1ux9: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(21 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1ux9.gif|left|200px]]<br />
<applet load="1ux9" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ux9, resolution 2.4&Aring;" />
'''MAPPING PROTEIN MATRIX CAVITIES IN HUMAN CYTOGLOBIN THROUGH XE ATOM BINDING: A CRYSTALLOGRAPHIC INVESTIGATION'''<br />


==Overview==
==Mapping protein matrix cavities in human cytoglobin through Xe atom binding: a crystallographic investigation==
Cytoglobin is the fourth recognized globin type, almost ubiquitously, distributed in human tissues; its function is still poorly understood., Cytoglobin displays a core region of about 150 residues, structurally, related to hemoglobin and myoglobin, and two extra segments, about 20, residues each, at the N- and C-termini. The core region hosts a large, apolar cavity, held to provide a ligand diffusion pathway to/from the, heme, and/or ligand temporary docking sites. Here we report the crystal, structure (2.4A resolution, R-factor 19.1%) of a human cytoglobin mutant, bearing the CysB2(38) --&gt; Ser and CysE9(83) --&gt; Ser substitutions (CYGB*), treated under pressurized xenon. Three Xe atoms bind to the heme distal, site region of CYGB* mapping the protein matrix apolar cavity. Despite ... [[http://ispc.weizmann.ac.il/pmbin/getpm?15044115 (full description)]]
<StructureSection load='1ux9' size='340' side='right'caption='[[1ux9]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ux9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UX9 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FC6:HEXACYANOFERRATE(3-)'>FC6</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</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=1ux9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ux9 OCA], [https://pdbe.org/1ux9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ux9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ux9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ux9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CYGB_HUMAN CYGB_HUMAN] May have a protective function during conditions of oxidative stress. May be involved in intracellular oxygen storage or transfer.
== 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/ux/1ux9_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=1ux9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cytoglobin is the fourth recognized globin type, almost ubiquitously distributed in human tissues; its function is still poorly understood. Cytoglobin displays a core region of about 150 residues, structurally related to hemoglobin and myoglobin, and two extra segments, about 20 residues each, at the N- and C-termini. The core region hosts a large apolar cavity, held to provide a ligand diffusion pathway to/from the heme, and/or ligand temporary docking sites. Here we report the crystal structure (2.4A resolution, R-factor 19.1%) of a human cytoglobin mutant bearing the CysB2(38) --&gt; Ser and CysE9(83) --&gt; Ser substitutions (CYGB*), treated under pressurized xenon. Three Xe atoms bind to the heme distal site region of CYGB* mapping the protein matrix apolar cavity. Despite the conserved globin fold, the cavity found in CYGB* is structured differently from those recognized to play a functional role in myoglobin, neuroglobin, truncated hemoglobins, and Cerebratulus lacteus mini-hemoglobin.


==About this Structure==
Mapping protein matrix cavities in human cytoglobin through Xe atom binding.,de Sanctis D, Dewilde S, Pesce A, Moens L, Ascenzi P, Hankeln T, Burmester T, Bolognesi M Biochem Biophys Res Commun. 2004 Apr 16;316(4):1217-21. PMID:15044115<ref>PMID:15044115</ref>
1UX9 is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]] with XE, HEM and FC6 as [[http://en.wikipedia.org/wiki/ligands ligands]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UX9 OCA]].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Mapping protein matrix cavities in human cytoglobin through Xe atom binding., de Sanctis D, Dewilde S, Pesce A, Moens L, Ascenzi P, Hankeln T, Burmester T, Bolognesi M, Biochem Biophys Res Commun. 2004 Apr 16;316(4):1217-21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15044115 15044115]
</div>
<div class="pdbe-citations 1ux9" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Ascenzi, P.]]
[[Category: Ascenzi P]]
[[Category: Bolognesi, M.]]
[[Category: Bolognesi M]]
[[Category: Burmester, T.]]
[[Category: Burmester T]]
[[Category: Dewilde, S.]]
[[Category: De Sanctis D]]
[[Category: Hankeln, T.]]
[[Category: Dewilde S]]
[[Category: Moens, L.]]
[[Category: Hankeln T]]
[[Category: Pesce, A.]]
[[Category: Moens L]]
[[Category: Sanctis, D.De.]]
[[Category: Pesce A]]
[[Category: FC6]]
[[Category: HEM]]
[[Category: XE]]
[[Category: heme]]
[[Category: oxygen storage/transport]]
[[Category: transport]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 13:14:48 2007''

Latest revision as of 12:06, 9 May 2024

Mapping protein matrix cavities in human cytoglobin through Xe atom binding: a crystallographic investigationMapping protein matrix cavities in human cytoglobin through Xe atom binding: a crystallographic investigation

Structural highlights

1ux9 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CYGB_HUMAN May have a protective function during conditions of oxidative stress. May be involved in intracellular oxygen storage or transfer.

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

Cytoglobin is the fourth recognized globin type, almost ubiquitously distributed in human tissues; its function is still poorly understood. Cytoglobin displays a core region of about 150 residues, structurally related to hemoglobin and myoglobin, and two extra segments, about 20 residues each, at the N- and C-termini. The core region hosts a large apolar cavity, held to provide a ligand diffusion pathway to/from the heme, and/or ligand temporary docking sites. Here we report the crystal structure (2.4A resolution, R-factor 19.1%) of a human cytoglobin mutant bearing the CysB2(38) --> Ser and CysE9(83) --> Ser substitutions (CYGB*), treated under pressurized xenon. Three Xe atoms bind to the heme distal site region of CYGB* mapping the protein matrix apolar cavity. Despite the conserved globin fold, the cavity found in CYGB* is structured differently from those recognized to play a functional role in myoglobin, neuroglobin, truncated hemoglobins, and Cerebratulus lacteus mini-hemoglobin.

Mapping protein matrix cavities in human cytoglobin through Xe atom binding.,de Sanctis D, Dewilde S, Pesce A, Moens L, Ascenzi P, Hankeln T, Burmester T, Bolognesi M Biochem Biophys Res Commun. 2004 Apr 16;316(4):1217-21. PMID:15044115[1]

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

References

  1. ↑ de Sanctis D, Dewilde S, Pesce A, Moens L, Ascenzi P, Hankeln T, Burmester T, Bolognesi M. Mapping protein matrix cavities in human cytoglobin through Xe atom binding. Biochem Biophys Res Commun. 2004 Apr 16;316(4):1217-21. PMID:15044115 doi:http://dx.doi.org/10.1016/j.bbrc.2004.03.007

1ux9, resolution 2.40Å

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=1ux9&oldid=4143738"