4eid: Difference between revisions

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 <StructureSection load='4eid' size='340' side='right'caption='[[4eid]], [[Resolution|resolution]] 1.13&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4eid]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agmenellum_quadruplicatum Agmenellum quadruplicatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EID FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4eid]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_sp._PCC_7002 Synechococcus sp. PCC 7002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EID FirstGlance]. <br>
-</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>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 1.13&#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;'>[[3dr0|3dr0]], [[4eic|4eic]], [[4eie|4eie]], [[4eif|4eif]]</div></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>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">petJ, petJ1, SYNPCC7002_A0167 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=32049 Agmenellum quadruplicatum])</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=4eid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eid OCA], [https://pdbe.org/4eid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eid RCSB], [https://www.ebi.ac.uk/pdbsum/4eid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eid ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CYC6_SYNP2 CYC6_SYNP2]] Functions as an electron carrier between membrane-bound cytochrome b6-f and photosystem I in oxygenic photosynthesis (By similarity).
+[https://www.uniprot.org/uniprot/CYC6_PICP2 CYC6_PICP2] Functions as an electron carrier between membrane-bound cytochrome b6-f and photosystem I in oxygenic photosynthesis.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
-The structure of the reduced form of cytochrome c(6) from the mesophilic cyanobacterium Synechococcus sp. PCC 7002 has been determined at 1.2 A and refined to an R-factor of 0.107. This protein is unique among all known cytochromes c(6), owing to the presence of an unusual seven-residue insertion, KDGSKSL(44-50), which differs from the insertion found in the recently discovered plant cytochromes c(6A). Furthermore, the present protein is unusual because of its very high content (36%) of the smallest residues (glycine and alanine). The structure reveals that the overall fold of the protein is similar to that of other class I c-type cytochromes, despite the presence of the specific insertion. The insertion is located within the most variable region of the cytochrome c(6) sequence, i.e. between helices II and III. The first six residues [KDGSKS(44-49)] form a loop, whereas the last residue, Leu50, extends the N-terminal beginning of helix III. Several specific noncovalent interactions are found inside the insertion, as well as between the insertion and the rest of the protein. The crystal structure contains three copies of the cytochrome c(6) molecule per asymmetric unit, and is characterized by an unusually high packing density, with solvent occupying barely 17.58% of the crystal volume.
+The cyanobacterium Synechococcus sp. PCC 7002 carries two genes, petJ1 and petJ2, for proteins related to soluble, cytochrome c6 electron transfer proteins. PetJ1 was purified from the cyanobacterium, and both cytochromes were expressed with heme incorporation in Escherichia coli. The expressed PetJ1 displayed spectral and biochemical properties virtually identical to those of PetJ1 from Synechococcus. PetJ1 is a typical cytochrome c6 but contains an unusual KDGSKSL insertion. PetJ2 isolated from E. coli exhibited absorbance spectra characteristic of cytochromes, although the alpha, beta, and gamma bands were red-shifted relative to those of PetJ1. Moreover, the surface electrostatic properties and redox midpoint potential of PetJ2 (pI 9.7; E(m,7) = 148 +/- 1.7 mV) differed substantially from those of PetJ1 (pI 3.8; E(m,7) = 319 +/- 1.6 mV). These data indicate that the PetJ2 cytochrome could not effectively replace PetJ1 as an electron acceptor for the cytochrome bf complex in photosynthesis. Phylogenetic comparisons against plant, algal, bacterial, and cyanobacterial genomes revealed two novel and widely distributed clusters of previously uncharacterized, cyanobacterial c 6-like cytochromes. PetJ2 belongs to a group that is distinct from both c6 cytochromes and the enigmatic chloroplast c 6A cytochromes. We tentatively designate the PetJ2 group as c6C cytochromes and the other new group as c6B cytochromes. Possible functions of these cytochromes are discussed.
-Atomic-resolution structure of reduced cyanobacterial cytochrome c6 with an unusual sequence insertion.,Bialek W, Krzywda S, Jaskolski M, Szczepaniak A FEBS J. 2009 Aug;276(16):4426-36. PMID:19678839<ref>PMID:19678839</ref>
+Deeply branching c6-like cytochromes of cyanobacteria.,Bialek W, Nelson M, Tamiola K, Kallas T, Szczepaniak A Biochemistry. 2008 May 20;47(20):5515-22. Epub 2008 Apr 26. PMID:018439023<ref>PMID:018439023</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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 ==See Also==
-*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
 *[[Cytochrome f 3D structures|Cytochrome f 3D structures]]
 == References ==
@@ Line 28: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Agmenellum quadruplicatum]]
 [[Category: Large Structures]]
-[[Category: Bialek, W]]
+[[Category: Synechococcus sp. PCC 7002]]
-[[Category: Jaskolski, M]]
+[[Category: Bialek W]]
-[[Category: Krzywda, S]]
+[[Category: Jaskolski M]]
-[[Category: Szczepaniak, A]]
+[[Category: Krzywda S]]
-[[Category: Zatwarnicki, P]]
+[[Category: Szczepaniak A]]
-[[Category: Cytochrome c6]]
+[[Category: Zatwarnicki P]]
-[[Category: Electron transport]]