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| | ==Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex== | | ==Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex== |
| - | <StructureSection load='5h7d' size='340' side='right' caption='[[5h7d]], [[Resolution|resolution]] 2.57Å' scene=''> | + | <StructureSection load='5h7d' size='340' side='right'caption='[[5h7d]], [[Resolution|resolution]] 2.57Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5h7d]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H7D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5h7d]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans], [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12], [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H7D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.57Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5h75|5h75]], [[5h76|5h76]], [[5h77|5h77]], [[5h78|5h78]], [[5h79|5h79]], [[5h7a|5h7a]], [[5h7b|5h7b]], [[5h7c|5h7c]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">spa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), cmd-1, T21H3.3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=32630 SYNTHETIC CONSTRUCT sequences])</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=5h7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7d OCA], [https://pdbe.org/5h7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h7d RCSB], [https://www.ebi.ac.uk/pdbsum/5h7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7d ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Putrescine_aminotransferase Putrescine aminotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.82 2.6.1.82] </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=5h7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7d OCA], [http://pdbe.org/5h7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7d RCSB], [http://www.ebi.ac.uk/pdbsum/5h7d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7d ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PAT_ECOLI PAT_ECOLI]] Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. Is also able to transaminate cadaverine and, in lower extent, spermidine, but not ornithine. Alpha-ketobutyrate and pyruvate can also act as amino acceptors, although much less efficiently.<ref>PMID:12617754</ref> | + | [https://www.uniprot.org/uniprot/PAT_ECOLI PAT_ECOLI] Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. Is also able to transaminate cadaverine and, in lower extent, spermidine, but not ornithine. Alpha-ketobutyrate and pyruvate can also act as amino acceptors, although much less efficiently.<ref>PMID:12617754</ref> [https://www.uniprot.org/uniprot/SPA_STAAU SPA_STAAU] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Putrescine aminotransferase]] | + | [[Category: Caenorhabditis elegans]] |
| - | [[Category: Synthetic construct sequences]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Kim, J H]] | + | [[Category: Large Structures]] |
| - | [[Category: Kwon, N Y]] | + | [[Category: Staphylococcus aureus]] |
| - | [[Category: Lee, H]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Lee, J H]] | + | [[Category: Kim JH]] |
| - | [[Category: Lee, J O]] | + | [[Category: Kwon NY]] |
| - | [[Category: Youn, S J]] | + | [[Category: Lee H]] |
| - | [[Category: Immune system-metal binding protein complex]] | + | [[Category: Lee JH]] |
| - | [[Category: Synthetic protein]] | + | [[Category: Lee JO]] |
| - | [[Category: Transferase]] | + | [[Category: Youn SJ]] |
| Structural highlights
Function
PAT_ECOLI Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. Is also able to transaminate cadaverine and, in lower extent, spermidine, but not ornithine. Alpha-ketobutyrate and pyruvate can also act as amino acceptors, although much less efficiently.[1] SPA_STAAU
Publication Abstract from PubMed
Generating artificial protein assemblies with complex shapes requires a method for connecting protein components with stable and predictable structures. Currently available methods for creating rigid protein assemblies rely on either complicated calculations or extensive trial and error. We describe a simple and efficient method for connecting two proteins via a fused alpha helix that is formed by joining two preexisting helices into a single extended helix. Because the end-to-end ligation of helices does not guarantee the formation of a continuous helix, we superimposed 1-2 turns of pairs of connecting helices by using a molecular graphics program. Then, we chose amino acids from the two natural sequences that would stabilize the connecting helix. This "shared helix method" is highly efficient. All the designed proteins that could be produced in Escherichia coli were readily crystallized and had the expected fusion structures. To prove the usefulness of this method, we produced two novel repeat proteins by assembling several copies of natural or artificial proteins with alpha helices at both termini. Their crystal structures demonstrated the successful assembly of the repeating units with the intended curved shapes. We propose that this method could dramatically expand the available repertoire of natural repeat proteins.
Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.,Youn SJ, Kwon NY, Lee JH, Kim JH, Choi J, Lee H, Lee JO Sci Rep. 2017 Jun 1;7(1):2595. doi: 10.1038/s41598-017-02803-z. PMID:28572639[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Samsonova NN, Smirnov SV, Altman IB, Ptitsyn LR. Molecular cloning and characterization of Escherichia coli K12 ygjG gene. BMC Microbiol. 2003 Jan 31;3(1):2. PMID:12617754
- ↑ Youn SJ, Kwon NY, Lee JH, Kim JH, Choi J, Lee H, Lee JO. Construction of novel repeat proteins with rigid and predictable structures using a shared helix method. Sci Rep. 2017 Jun 1;7(1):2595. doi: 10.1038/s41598-017-02803-z. PMID:28572639 doi:http://dx.doi.org/10.1038/s41598-017-02803-z
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