1d4c: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:1d4c.png|left|200px]]


<!--
==CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1==
The line below this paragraph, containing "STRUCTURE_1d4c", creates the "Structure Box" on the page.
<StructureSection load='1d4c' size='340' side='right'caption='[[1d4c]], [[Resolution|resolution]] 2.90&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'>[[1d4c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D4C 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]] 2.9&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_1d4c|  PDB=1d4c  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d4c OCA], [https://pdbe.org/1d4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d4c RCSB], [https://www.ebi.ac.uk/pdbsum/1d4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d4c ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/FCCA_SHEON FCCA_SHEON] Flavocytochrome that catalyzes the reduction of fumarate to succinate (PubMed:12196158, PubMed:12899636, PubMed:22458729). Is essential for fumarate respiration during anaerobic growth, acting as the terminal reductase (By similarity). Receives electrons from the membrane-bound tetraheme c-type cytochrome CymA (PubMed:12196158, PubMed:12899636, PubMed:19837833, PubMed:22458729). Under ferric iron-reducing conditions, can be part of an electron transport chain to ferric iron, by accepting electrons from CymA and transfering them to the c-type cytochrome MtrA (PubMed:19837833). Also plays an important role in the reduction of selenite to elemental selenium (PubMed:24435070). May act as a transient electron storage protein (PubMed:19837833).[UniProtKB:Q07WU7]<ref>PMID:12196158</ref> <ref>PMID:12899636</ref> <ref>PMID:19837833</ref> <ref>PMID:22458729</ref> <ref>PMID:24435070</ref>
== 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/d4/1d4c_consurf.spt"</scriptWhenChecked>
    <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/main_output.php?pdb_ID=1d4c ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Fumarate respiration is one of the most widespread types of anaerobic respiration. The soluble fumarate reductase of Shewanella putrefaciens MR-1 is a periplasmic tetraheme flavocytochrome c. The crystal structures of the enzyme were solved to 2.9 A for the uncomplexed form and to 2.8 A and 2.5 A for the fumarate and the succinate-bound protein, respectively. The structures reveal a flexible capping domain linked to the FAD-binding domain. A catalytic mechanism for fumarate reduction based on the structure of the complexed protein is proposed. The mechanism for the reverse reaction is a model for the homologous succinate dehydrogenase (complex II) of the respiratory chain. In flavocytochrome c fumarate reductase, all redox centers are in van der Waals contact with one another, thus providing an efficient conduit of electrons from the hemes via the FAD to fumarate.


===CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1===
Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1.,Leys D, Tsapin AS, Nealson KH, Meyer TE, Cusanovich MA, Van Beeumen JJ Nat Struct Biol. 1999 Dec;6(12):1113-7. PMID:10581551<ref>PMID:10581551</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<!--
</div>
The line below this paragraph, {{ABSTRACT_PUBMED_10581551}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1d4c" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 10581551 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_10581551}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1D4C is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Shewanella_putrefaciens Shewanella putrefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D4C OCA].
[[Category: Shewanella oneidensis]]
 
[[Category: Cusanovich MA]]
==Reference==
[[Category: Leys D]]
Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1., Leys D, Tsapin AS, Nealson KH, Meyer TE, Cusanovich MA, Van Beeumen JJ, Nat Struct Biol. 1999 Dec;6(12):1113-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10581551 10581551]
[[Category: Meyer TE]]
[[Category: Shewanella putrefaciens]]
[[Category: Tsapin AS]]
[[Category: Single protein]]
[[Category: Van Beeumen JJ]]
[[Category: Succinate dehydrogenase]]
[[Category: Beeumen, J J.Van.]]
[[Category: Cusanovich, M A.]]
[[Category: Leys, D.]]
[[Category: Meyer, T E.]]
[[Category: Tsapin, A S.]]
[[Category: Tetraheme flavocytochrome c]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:23:10 2008''

Latest revision as of 09:31, 30 October 2024

CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1

Structural highlights

1d4c is a 4 chain structure with sequence from Shewanella oneidensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.9Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FCCA_SHEON Flavocytochrome that catalyzes the reduction of fumarate to succinate (PubMed:12196158, PubMed:12899636, PubMed:22458729). Is essential for fumarate respiration during anaerobic growth, acting as the terminal reductase (By similarity). Receives electrons from the membrane-bound tetraheme c-type cytochrome CymA (PubMed:12196158, PubMed:12899636, PubMed:19837833, PubMed:22458729). Under ferric iron-reducing conditions, can be part of an electron transport chain to ferric iron, by accepting electrons from CymA and transfering them to the c-type cytochrome MtrA (PubMed:19837833). Also plays an important role in the reduction of selenite to elemental selenium (PubMed:24435070). May act as a transient electron storage protein (PubMed:19837833).[UniProtKB:Q07WU7][1] [2] [3] [4] [5]

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

Fumarate respiration is one of the most widespread types of anaerobic respiration. The soluble fumarate reductase of Shewanella putrefaciens MR-1 is a periplasmic tetraheme flavocytochrome c. The crystal structures of the enzyme were solved to 2.9 A for the uncomplexed form and to 2.8 A and 2.5 A for the fumarate and the succinate-bound protein, respectively. The structures reveal a flexible capping domain linked to the FAD-binding domain. A catalytic mechanism for fumarate reduction based on the structure of the complexed protein is proposed. The mechanism for the reverse reaction is a model for the homologous succinate dehydrogenase (complex II) of the respiratory chain. In flavocytochrome c fumarate reductase, all redox centers are in van der Waals contact with one another, thus providing an efficient conduit of electrons from the hemes via the FAD to fumarate.

Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1.,Leys D, Tsapin AS, Nealson KH, Meyer TE, Cusanovich MA, Van Beeumen JJ Nat Struct Biol. 1999 Dec;6(12):1113-7. PMID:10581551[6]

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

References

  1. ↑ Schwalb C, Chapman SK, Reid GA. The membrane-bound tetrahaem c-type cytochrome CymA interacts directly with the soluble fumarate reductase in Shewanella. Biochem Soc Trans. 2002 Aug;30(4):658-62. PMID:12196158 doi:10.1042/bst0300658
  2. ↑ Schwalb C, Chapman SK, Reid GA. The tetraheme cytochrome CymA is required for anaerobic respiration with dimethyl sulfoxide and nitrite in Shewanella oneidensis. Biochemistry. 2003 Aug 12;42(31):9491-7. PMID:12899636 doi:10.1021/bi034456f
  3. ↑ Schuetz B, Schicklberger M, Kuermann J, Spormann AM, Gescher J. Periplasmic electron transfer via the c-type cytochromes MtrA and FccA of Shewanella oneidensis MR-1. Appl Environ Microbiol. 2009 Dec;75(24):7789-96. PMID:19837833 doi:10.1128/AEM.01834-09
  4. ↑ Marritt SJ, Lowe TG, Bye J, McMillan DG, Shi L, Fredrickson J, Zachara J, Richardson DJ, Cheesman MR, Jeuken LJ, Butt JN. A functional description of CymA, an electron-transfer hub supporting anaerobic respiratory flexibility in Shewanella. Biochem J. 2012 Jun 15;444(3):465-74. PMID:22458729 doi:10.1042/BJ20120197
  5. ↑ Li DB, Cheng YY, Wu C, Li WW, Li N, Yang ZC, Tong ZH, Yu HQ. Selenite reduction by Shewanella oneidensis MR-1 is mediated by fumarate reductase in periplasm. Sci Rep. 2014 Jan 17;4:3735. PMID:24435070 doi:10.1038/srep03735
  6. ↑ Leys D, Tsapin AS, Nealson KH, Meyer TE, Cusanovich MA, Van Beeumen JJ. Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1. Nat Struct Biol. 1999 Dec;6(12):1113-7. PMID:10581551 doi:http://dx.doi.org/10.1038/70051

1d4c, resolution 2.90Å

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=1d4c&oldid=4198053"