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| | ==Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal== | | ==Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal== |
| - | <StructureSection load='5h8y' size='340' side='right' caption='[[5h8y]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='5h8y' size='340' side='right'caption='[[5h8y]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5h8y]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H8Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5h8y]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H8Y FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SRM:SIROHEME'>SRM</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b2f|3b2f]], [[5h8v|5h8v]], [[5h92|5h92]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SRM:SIROHEME'>SRM</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Assimilatory_sulfite_reductase_(ferredoxin) Assimilatory sulfite reductase (ferredoxin)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.7.1 1.8.7.1] </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=5h8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8y OCA], [https://pdbe.org/5h8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h8y RCSB], [https://www.ebi.ac.uk/pdbsum/5h8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8y ProSAT]</span></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=5h8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8y OCA], [http://pdbe.org/5h8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h8y RCSB], [http://www.ebi.ac.uk/pdbsum/5h8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8y ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SIR_MAIZE SIR_MAIZE]] Essential protein with sulfite reductase activity required in assimilatory sulfate reduction pathway during both primary and secondary metabolism and thus involved in development and growth.<ref>PMID:10712553</ref> <ref>PMID:11163356</ref> <ref>PMID:14871491</ref> <ref>PMID:17371503</ref> DNA-binding protein that binds to both double-stranded and single-stranded DNA without significant sequence specificity to reversibly repress the transcriptional activity of chloroplast nucleoids by promoting DNA compaction and possibly regulate DNA replication.<ref>PMID:11163356</ref> [[http://www.uniprot.org/uniprot/FER1_MAIZE FER1_MAIZE]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. | + | [https://www.uniprot.org/uniprot/SIR_MAIZE SIR_MAIZE] Essential protein with sulfite reductase activity required in assimilatory sulfate reduction pathway during both primary and secondary metabolism and thus involved in development and growth.<ref>PMID:10712553</ref> <ref>PMID:11163356</ref> <ref>PMID:14871491</ref> <ref>PMID:17371503</ref> DNA-binding protein that binds to both double-stranded and single-stranded DNA without significant sequence specificity to reversibly repress the transcriptional activity of chloroplast nucleoids by promoting DNA compaction and possibly regulate DNA replication.<ref>PMID:11163356</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5h8y" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5h8y" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ferredoxin 3D structures|Ferredoxin 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Hase, T]] | + | [[Category: Large Structures]] |
| - | [[Category: Kurisu, G]] | + | [[Category: Zea mays]] |
| - | [[Category: Nakayama, M]] | + | [[Category: Hase T]] |
| - | [[Category: Ferredoxin]] | + | [[Category: Kurisu G]] |
| - | [[Category: Oxidoreductase-electron transport complex]] | + | [[Category: Nakayama M]] |
| - | [[Category: Sulfite reductase]]
| + | |
| Structural highlights
5h8y is a 6 chain structure with sequence from Zea mays. 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
SIR_MAIZE Essential protein with sulfite reductase activity required in assimilatory sulfate reduction pathway during both primary and secondary metabolism and thus involved in development and growth.[1] [2] [3] [4] DNA-binding protein that binds to both double-stranded and single-stranded DNA without significant sequence specificity to reversibly repress the transcriptional activity of chloroplast nucleoids by promoting DNA compaction and possibly regulate DNA replication.[5]
Publication Abstract from PubMed
The structure of the complex of maize sulfite reductase (SiR) and ferredoxin (Fd) has been determined by X-ray crystallography. Co-crystals of the two proteins prepared under different conditions were subjected to the diffraction analysis and three possible structures of the complex were solved. Although topological relationship of SiR and Fd varied in each of the structures, two characteristics common to all structures were found in the pattern of protein-protein interactions and positional arrangements of redox centres; (i) a few negative residues of Fd contact with a narrow area of SiR with positive electrostatic surface potential and (ii) [2Fe-2S] cluster of Fd and [4Fe-4S] cluster of SiR are in a close proximity with the shortest distance around 12 A. Mutational analysis of a total of seven basic residues of SiR distributed widely at the interface of the complex showed their importance for supporting an efficient Fd-dependent activity and a strong physical binding to Fd. These combined results suggest that the productive electron transfer complex of SiR and Fd could be formed through multiple processes of the electrostatic intermolecular interaction and this implication is discussed in terms of the multi-functionality of Fd in various redox metabolisms.
Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin.,Kim JY, Nakayama M, Toyota H, Kurisu G, Hase T J Biochem. 2016 Feb 26. pii: mvw016. PMID:26920048[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yonekura-Sakakibara K, Onda Y, Ashikari T, Tanaka Y, Kusumi T, Hase T. Analysis of reductant supply systems for ferredoxin-dependent sulfite reductase in photosynthetic and nonphotosynthetic organs of maize. Plant Physiol. 2000 Mar;122(3):887-94. PMID:10712553
- ↑ Sato N, Nakayama M, Hase T. The 70-kDa major DNA-compacting protein of the chloroplast nucleoid is sulfite reductase. FEBS Lett. 2001 Jan 5;487(3):347-50. PMID:11163356
- ↑ Hirasawa M, Nakayama M, Hase T, Knaff DB. Oxidation-reduction properties of maize ferredoxin: sulfite oxidoreductase. Biochim Biophys Acta. 2004 Feb 15;1608(2-3):140-8. PMID:14871491 doi:http://dx.doi.org/10.1016/j.bbabio.2003.11.004
- ↑ Sekine K, Fujiwara M, Nakayama M, Takao T, Hase T, Sato N. DNA binding and partial nucleoid localization of the chloroplast stromal enzyme ferredoxin:sulfite reductase. FEBS J. 2007 Apr;274(8):2054-69. Epub 2007 Mar 19. PMID:17371503 doi:http://dx.doi.org/EJB5748
- ↑ Sato N, Nakayama M, Hase T. The 70-kDa major DNA-compacting protein of the chloroplast nucleoid is sulfite reductase. FEBS Lett. 2001 Jan 5;487(3):347-50. PMID:11163356
- ↑ Kim JY, Nakayama M, Toyota H, Kurisu G, Hase T. Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin. J Biochem. 2016 Feb 26. pii: mvw016. PMID:26920048 doi:http://dx.doi.org/10.1093/jb/mvw016
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