Proteopedia - User contributions [en]

https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Nicole+R+Pendini Proteopedia - User contributions [en] 2026-09-23T18:42:22Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=640315 Biotin Protein Ligase 2008-07-12T12:08:42Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of [http://en.wikipedia.org/wiki/Biotin biotin] onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. <br /> <br /> Biotinylation is catalysed through a two-step reaction where biotin is first activated to biotinyl-5′-AMP in an ATP dependent manner. The biotin is then transferred onto the ε-amino group of a specific target lysine residue. The reaction mechanism is related to that of amino acyl-tRNA synthetases and lipoyl ligases where the reaction proceeds through the formation of an adenylated intermediate, suggesting a common ancestral relationship <ref> [http://www.ncbi.nlm.nih.gov/pubmed/18442489 Pendini, 2008] </ref> . <br /> <br /> Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 <ref> [http://www.ncbi.nlm.nih.gov/pubmed/16510991 Bagautdinov B, 2005]</ref> have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure <ref> [http://www.ncbi.nlm.nih.gov/pubmed/1409631 wilson, 1992]</ref>. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/3'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> Upon biotin binding, the protein homodimerises and the unstructured loops become more ordered.<br /> <br /> <br /> <br /> <br /> ==References==<br /> <references/></div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=640314 Biotin Protein Ligase 2008-07-12T11:54:25Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of [http://en.wikipedia.org/wiki/Biotin biotin] onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. <br /> <br /> Biotinylation is catalysed through a two-step reaction where biotin is first activated to biotinyl-5′-AMP in an ATP dependent manner. The biotin is then transferred onto the ε-amino group of a specific target lysine residue. The reaction mechanism is related to that of amino acyl-tRNA synthetases and lipoyl ligases where the reaction proceeds through the formation of an adenylated intermediate, suggesting a common ancestral relationship <ref> [http://www.ncbi.nlm.nih.gov/pubmed/18442489 Pendini, 2008] </ref> . <br /> <br /> Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 <ref> [http://www.ncbi.nlm.nih.gov/pubmed/16510991 Bagautdinov B, 2005]</ref> have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure <ref> [http://www.ncbi.nlm.nih.gov/pubmed/1409631 wilson, 1992]</ref>. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/3'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> Upon [biotin] binding, the protein homodimerises and the unstructured loops become more ordered.<br /> <br /> <br /> <br /> <br /> ==References==<br /> <references/></div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=640313 Biotin Protein Ligase 2008-07-12T11:33:01Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of [http://en.wikipedia.org/wiki/Biotin biotin] onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 <ref> [http://www.ncbi.nlm.nih.gov/pubmed/16510991 Bagautdinov B, 2005]</ref> have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure <ref> [http://www.ncbi.nlm.nih.gov/pubmed/1409631 wilson, 1992]</ref>. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/3'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> Upon [biotin] binding, the protein homodimerises and the unstructured loops become more ordered.<br /> <br /> <br /> ==References==<br /> <references/></div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=640312 Biotin Protein Ligase 2008-07-12T11:32:11Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of [http://en.wikipedia.org/wiki/Biotin biotin] onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 <ref> [http://www.ncbi.nlm.nih.gov/pubmed/16510991]</ref> have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure <ref> [http://www.ncbi.nlm.nih.gov/pubmed/1409631 wilson, 1992]</ref>. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/3'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> Upon [biotin] binding, the protein homodimerises and the unstructured loops become more ordered.<br /> <br /> <br /> ==References==<br /> <references/></div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=546792 Biotin Protein Ligase 2008-06-07T09:36:41Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of [http://en.wikipedia.org/wiki/Biotin biotin] onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure <ref> [http://www.ncbi.nlm.nih.gov/pubmed/1409631 wilson, 1992]</ref>. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/3'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> Upon [biotin] binding, the protein homodimerises and the unstructured loops become more ordered.<br /> <br /> <br /> ==References==<br /> <references/></div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=546791 Biotin Protein Ligase 2008-06-07T09:33:43Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure <ref> [http://www.ncbi.nlm.nih.gov/pubmed/1409631 wilson, 1992]</ref>. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/3'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> Upon [biotin] binding, the protein homodimerises and the unstructured loops become more ordered.<br /> <br /> <br /> ==References==<br /> <references/></div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=546788 Biotin Protein Ligase 2008-06-07T09:29:39Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure <ref>wilson, 1992</ref>. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/3'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> Upon [biotin] binding, the protein homodimerises and the unstructured loops become more ordered.<br /> <br /> <br /> ==References==<br /> <references/></div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=546787 Biotin Protein Ligase 2008-06-07T09:28:41Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure <ref>wilson, 1992</ref>. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/3'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> Upon [biotin] binding, the protein homodimerises and the unstructured loops become more ordered.<br /> <br /> <br /> ==References==</div>

Nicole R Pendini https://proteopedia.org/index.php?title=User:Nicole_R_Pendini&diff=546785 User:Nicole R Pendini 2008-06-07T09:12:41Z

<p>Nicole R Pendini: </p> <hr /> <div>[[Image:Nicole.JPG | right]]Currently at the department of Biochemistry at Monash University in Melbourne Australia to finish my PhD.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=User:Nicole_R_Pendini&diff=546784 User:Nicole R Pendini 2008-06-07T09:11:34Z

<p>Nicole R Pendini: </p> <hr /> <div>[[Image:Nicole.JPG]]Currently at the department of Biochemistry at Monash University in Melbourne Australia to finish my PhD.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=User:Nicole_R_Pendini&diff=546783 User:Nicole R Pendini 2008-06-07T09:01:02Z

<p>Nicole R Pendini: </p> <hr /> <div>[[Image:Nicole.jpg]]Currently at the department of Biochemistry at Monash University in Melbourne Australia to finish my PhD.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=File:Nicole.JPG&diff=546782 File:Nicole.JPG 2008-06-07T08:59:50Z

<p>Nicole R Pendini: </p> <hr /> <div></div>

Nicole R Pendini https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=546775 User talk:Eran Hodis 2008-06-07T08:07:01Z

<p>Nicole R Pendini: </p> <hr /> <div>Dear Eran,<br /> <br /> The email tag trick is interesting and I didn't know about it. However, it seems to me that it would not protect the email address since it remains in a form recognizable to worms in the page source and any user can view source too. I don't worry about my own email. I started putting it plainly in all my web pages in 1995, and I continue to do so. At this point, the spam control on my email system is so good that it causes no problem. However, I try to be careful never to put anyone else's email on a website in plain form. [[User:Eric Martz|Eric Martz]]<br /> <br /> Eran-<br /> Let's see how my attempts to figure out "user talk" go. I have been meaning to get back to you for a long time, but as you can see, it hasn't happened until now. It was a good experience to work on Proteopedia and interesting how the page I made would change without me knowing it as things were worked out on your end. Karl shared with me how you have been sharing the Photosystem II page in Italy. It was surprising to me to find that others were interested in seeing it too, but that's the point of it all! The interface Proteopedia has for J-mol is definitely better than many others. My classmates were all jealous that I got to use Proteopedia and they had to use other, more clunky interfaces. <br /> One thing that I attempted and couldn't figure out was labeling. Photosystem II has a lot of ligands and my attempts to label them as well as other individual atoms resulted in the labeling of every atom! Maybe I was just missing something, but that could be something to work on. Another feature which might be helpful would be a representations "reset" button. Sometimes, I would try things and then not like them, but since the original settings aren't given, it took a more round about approach to return to the original view. Reset would just make things easier. <br /> Thanks for letting me be a part of Proteopedia. <br /> -Emily Forschler<br /> [[User:Emily Forschler|Emily Forschler]] 17:48, 3 June 2008 (EDT)<br /> <br /> <br /> <br /> Dear Eran, please see Sandbox 30. We uploaded a file from PQS. The filename is 1nsb_mmol.pdb. We tried to display it in Jmol on Sandbox 30 but failed. Please help us, thanks, -Eric in Osaka<br /> <br /> Hi Eran, I was wanting to delete the extra "Tom Garrett" page but could not see ho to delete a page Is this possible... Tom<br /> <br /> Hey Eran, we were locked in the discussion hall, would you have time tomorrow at coffee break 11am? Nicole Pendini<br /> <br /> getting technical now (does this work)? [[User:Nicole R Pendini|Nicole R Pendini]] 11:07, 7 June 2008 (IDT)</div>

Nicole R Pendini https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=546766 User talk:Eran Hodis 2008-06-06T16:48:36Z

<p>Nicole R Pendini: </p> <hr /> <div>Dear Eran,<br /> <br /> The email tag trick is interesting and I didn't know about it. However, it seems to me that it would not protect the email address since it remains in a form recognizable to worms in the page source and any user can view source too. I don't worry about my own email. I started putting it plainly in all my web pages in 1995, and I continue to do so. At this point, the spam control on my email system is so good that it causes no problem. However, I try to be careful never to put anyone else's email on a website in plain form. [[User:Eric Martz|Eric Martz]]<br /> <br /> Eran-<br /> Let's see how my attempts to figure out "user talk" go. I have been meaning to get back to you for a long time, but as you can see, it hasn't happened until now. It was a good experience to work on Proteopedia and interesting how the page I made would change without me knowing it as things were worked out on your end. Karl shared with me how you have been sharing the Photosystem II page in Italy. It was surprising to me to find that others were interested in seeing it too, but that's the point of it all! The interface Proteopedia has for J-mol is definitely better than many others. My classmates were all jealous that I got to use Proteopedia and they had to use other, more clunky interfaces. <br /> One thing that I attempted and couldn't figure out was labeling. Photosystem II has a lot of ligands and my attempts to label them as well as other individual atoms resulted in the labeling of every atom! Maybe I was just missing something, but that could be something to work on. Another feature which might be helpful would be a representations "reset" button. Sometimes, I would try things and then not like them, but since the original settings aren't given, it took a more round about approach to return to the original view. Reset would just make things easier. <br /> Thanks for letting me be a part of Proteopedia. <br /> -Emily Forschler<br /> [[User:Emily Forschler|Emily Forschler]] 17:48, 3 June 2008 (EDT)<br /> <br /> <br /> <br /> Dear Eran, please see Sandbox 30. We uploaded a file from PQS. The filename is 1nsb_mmol.pdb. We tried to display it in Jmol on Sandbox 30 but failed. Please help us, thanks, -Eric in Osaka<br /> <br /> Hi Eran, I was wanting to delete the extra "Tom Garrett" page but could not see ho to delete a page Is this possible... Tom<br /> <br /> Hey Eran, we were locked in the discussion hall, would you have time tomorrow at coffee break 11am? Nicole Pendini</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=546763 Biotin Protein Ligase 2008-06-06T16:39:36Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/3'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> Upon [biotin] binding, the protein homodimerises and the unstructured loops become more ordered.<br /> <br /> <br /> ==References==</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=546753 Biotin Protein Ligase 2008-06-06T15:46:36Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/2'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.<br /> <br /> <br /> ==References==</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=546752 Biotin Protein Ligase 2008-06-06T15:42:00Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/2'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=546748 Biotin Protein Ligase 2008-06-06T15:38:05Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1bia | PDB=1bia | SCENE=}}<br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/1'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Rop_protein&diff=546743 Rop protein 2008-06-06T15:30:36Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1rop | PDB=1rop | SCENE=Rop_protein/Wt_rop/1}}<scene name='Rop_protein/Wt_rop/1'>Rop</scene> (Repressor Of Primer) is a small homodimeric RNA-binding protein that is involved in the regulation of copy number of the ColE1 plasmids of E.coli, where it is encoded<ref>Polisky, 1988</ref>. Its structure has been studied using both X-ray crystallography (Banner ''et al.'', 1987) and NMR (Eberle ''et al''., 1991). <br /> Each monomer has molecular weight of 14456 Da and it is consisted of 63 amino acids that forms two α-helices connected by <scene name='Rop_protein/Wt_rop_loop/2'> a loop </scene>of four amino acids (L29, D30, A31, D32). The two monomers are related with a 2-fold symmetry axis. <br /> <br /> ==4-α-helical bundle==<br /> Rop is the paradigm of a canonical 4-α-helical bundle and its apparent structural simplicity of its folding rendered it as model system to investigate the sequence-structure relationships in the folding and dynamics of 4-α-helix. The four α-helices are amphipathic, pack in an antiparallel fashion and display a specific pattern of hydrophobic and hydrophilic amino acids, of the type (a,b,c,d,e,f,g)n, which is repeated every seven residues (heptad pattern). Positions a and d are generally hydrophobic and the side chains of these residues are packed in the central part of the structure according to the “knobs in holes” model forming the hydrophobic core. The heptad periodicity in the sequence of Rop is disrupted only once and leads to the formation of the loop. <scene name='Rop_protein/Wt_rop_a31/2'>Ala31</scene> has a crucial role in the formation of the loop region as it is the only amino acid that simultaneously forms hydrogen bond to both helices.<br /> <br /> == Mutants ==<br /> Numerous mutations in the loop region of Rop have been produced:<br /> *deletion of 5 a/a of loop ([[1qx8]])<br /> *site-directed mutants in loop <br /> *replacement and insertion of glycine residues in loop <br /> *restored of heptad pattern in loop region) ([[1nkd]])<br /> *a single alanine to proline substitution ([[1b6q]]) (Pro31, unlike Ala31, is more confor-mationally constrained, the dihedral angles of Ala31 in the wild type molecule are prohibited to Pro, and leads to a folding pathway for a thermodynamically less stable conformation.)<br /> *re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle([[1yo7]])<br /> *ALA2ILE2-6, repacted the hydrophobic core and a new fold ([[1f4n]])<br /> <br /> ==References==<br /> <references/><br /> <br /> {{Clear}}</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Rop_protein&diff=546741 Rop protein 2008-06-06T15:29:20Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1rop | PDB=1rop | SCENE=Rop_protein/Wt_rop/1}}<scene name='Rop_protein/Wt_rop/1'>Rop</scene> (Repressor Of Primer) is a small homodimeric RNA-binding protein that is involved in the regulation of copy number of the ColE1 plasmids of E.coli, where it is encoded<ref>[[Polisky]], 1988</ref>. Its structure has been studied using both X-ray crystallography (Banner ''et al.'', 1987) and NMR (Eberle ''et al''., 1991). <br /> Each monomer has molecular weight of 14456 Da and it is consisted of 63 amino acids that forms two α-helices connected by <scene name='Rop_protein/Wt_rop_loop/2'> a loop </scene>of four amino acids (L29, D30, A31, D32). The two monomers are related with a 2-fold symmetry axis. <br /> <br /> ==4-α-helical bundle==<br /> Rop is the paradigm of a canonical 4-α-helical bundle and its apparent structural simplicity of its folding rendered it as model system to investigate the sequence-structure relationships in the folding and dynamics of 4-α-helix. The four α-helices are amphipathic, pack in an antiparallel fashion and display a specific pattern of hydrophobic and hydrophilic amino acids, of the type (a,b,c,d,e,f,g)n, which is repeated every seven residues (heptad pattern). Positions a and d are generally hydrophobic and the side chains of these residues are packed in the central part of the structure according to the “knobs in holes” model forming the hydrophobic core. The heptad periodicity in the sequence of Rop is disrupted only once and leads to the formation of the loop. <scene name='Rop_protein/Wt_rop_a31/2'>Ala31</scene> has a crucial role in the formation of the loop region as it is the only amino acid that simultaneously forms hydrogen bond to both helices.<br /> <br /> == Mutants ==<br /> Numerous mutations in the loop region of Rop have been produced:<br /> *deletion of 5 a/a of loop ([[1qx8]])<br /> *site-directed mutants in loop <br /> *replacement and insertion of glycine residues in loop <br /> *restored of heptad pattern in loop region) ([[1nkd]])<br /> *a single alanine to proline substitution ([[1b6q]]) (Pro31, unlike Ala31, is more confor-mationally constrained, the dihedral angles of Ala31 in the wild type molecule are prohibited to Pro, and leads to a folding pathway for a thermodynamically less stable conformation.)<br /> *re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle([[1yo7]])<br /> *ALA2ILE2-6, repacted the hydrophobic core and a new fold ([[1f4n]])<br /> <br /> ==References==<br /> <references/><br /> <br /> {{Clear}}</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Rop_protein&diff=546740 Rop protein 2008-06-06T15:28:33Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1rop | PDB=1rop | SCENE=Rop_protein/Wt_rop/1}}<scene name='Rop_protein/Wt_rop/1'>Rop</scene> (Repressor Of Primer) is a small homodimeric RNA-binding protein that is involved in the regulation of copy number of the ColE1 plasmids of E.coli, where it is encoded<ref>[Polisky], 1988</ref>. Its structure has been studied using both X-ray crystallography (Banner ''et al.'', 1987) and NMR (Eberle ''et al''., 1991). <br /> Each monomer has molecular weight of 14456 Da and it is consisted of 63 amino acids that forms two α-helices connected by <scene name='Rop_protein/Wt_rop_loop/2'> a loop </scene>of four amino acids (L29, D30, A31, D32). The two monomers are related with a 2-fold symmetry axis. <br /> <br /> ==4-α-helical bundle==<br /> Rop is the paradigm of a canonical 4-α-helical bundle and its apparent structural simplicity of its folding rendered it as model system to investigate the sequence-structure relationships in the folding and dynamics of 4-α-helix. The four α-helices are amphipathic, pack in an antiparallel fashion and display a specific pattern of hydrophobic and hydrophilic amino acids, of the type (a,b,c,d,e,f,g)n, which is repeated every seven residues (heptad pattern). Positions a and d are generally hydrophobic and the side chains of these residues are packed in the central part of the structure according to the “knobs in holes” model forming the hydrophobic core. The heptad periodicity in the sequence of Rop is disrupted only once and leads to the formation of the loop. <scene name='Rop_protein/Wt_rop_a31/2'>Ala31</scene> has a crucial role in the formation of the loop region as it is the only amino acid that simultaneously forms hydrogen bond to both helices.<br /> <br /> == Mutants ==<br /> Numerous mutations in the loop region of Rop have been produced:<br /> *deletion of 5 a/a of loop ([[1qx8]])<br /> *site-directed mutants in loop <br /> *replacement and insertion of glycine residues in loop <br /> *restored of heptad pattern in loop region) ([[1nkd]])<br /> *a single alanine to proline substitution ([[1b6q]]) (Pro31, unlike Ala31, is more confor-mationally constrained, the dihedral angles of Ala31 in the wild type molecule are prohibited to Pro, and leads to a folding pathway for a thermodynamically less stable conformation.)<br /> *re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle([[1yo7]])<br /> *ALA2ILE2-6, repacted the hydrophobic core and a new fold ([[1f4n]])<br /> <br /> ==References==<br /> <references/><br /> <br /> {{Clear}}</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Rop_protein&diff=546739 Rop protein 2008-06-06T15:27:33Z

<p>Nicole R Pendini: </p> <hr /> <div>{{STRUCTURE_1rop | PDB=1rop | SCENE=Rop_protein/Wt_rop/1}}<scene name='Rop_protein/Wt_rop/1'>Rop</scene> (Repressor Of Primer) is a small homodimeric RNA-binding protein that is involved in the regulation of copy number of the ColE1 plasmids of E.coli, where it is encoded<ref>[Polisky, 1988]</ref>. Its structure has been studied using both X-ray crystallography (Banner ''et al.'', 1987) and NMR (Eberle ''et al''., 1991). <br /> Each monomer has molecular weight of 14456 Da and it is consisted of 63 amino acids that forms two α-helices connected by <scene name='Rop_protein/Wt_rop_loop/2'> a loop </scene>of four amino acids (L29, D30, A31, D32). The two monomers are related with a 2-fold symmetry axis. <br /> <br /> ==4-α-helical bundle==<br /> Rop is the paradigm of a canonical 4-α-helical bundle and its apparent structural simplicity of its folding rendered it as model system to investigate the sequence-structure relationships in the folding and dynamics of 4-α-helix. The four α-helices are amphipathic, pack in an antiparallel fashion and display a specific pattern of hydrophobic and hydrophilic amino acids, of the type (a,b,c,d,e,f,g)n, which is repeated every seven residues (heptad pattern). Positions a and d are generally hydrophobic and the side chains of these residues are packed in the central part of the structure according to the “knobs in holes” model forming the hydrophobic core. The heptad periodicity in the sequence of Rop is disrupted only once and leads to the formation of the loop. <scene name='Rop_protein/Wt_rop_a31/2'>Ala31</scene> has a crucial role in the formation of the loop region as it is the only amino acid that simultaneously forms hydrogen bond to both helices.<br /> <br /> == Mutants ==<br /> Numerous mutations in the loop region of Rop have been produced:<br /> *deletion of 5 a/a of loop ([[1qx8]])<br /> *site-directed mutants in loop <br /> *replacement and insertion of glycine residues in loop <br /> *restored of heptad pattern in loop region) ([[1nkd]])<br /> *a single alanine to proline substitution ([[1b6q]]) (Pro31, unlike Ala31, is more confor-mationally constrained, the dihedral angles of Ala31 in the wild type molecule are prohibited to Pro, and leads to a folding pathway for a thermodynamically less stable conformation.)<br /> *re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle([[1yo7]])<br /> *ALA2ILE2-6, repacted the hydrophobic core and a new fold ([[1f4n]])<br /> <br /> ==References==<br /> <references/><br /> <br /> {{Clear}}</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=545145 Biotin Protein Ligase 2008-06-03T13:33:17Z

<p>Nicole R Pendini: </p> <hr /> <div><applet load='1bia' size='500' frame='true' align='right' caption='The first structure of a Biotin Protein Ligase from E.coli' /><br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/1'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/2'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=545144 Biotin Protein Ligase 2008-06-03T13:31:26Z

<p>Nicole R Pendini: </p> <hr /> <div><applet load='1bia' size='500' frame='true' align='right' caption='The first structure of a Biotin Protein Ligase from E.coli' /><br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/1'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cterm/1'>C- terminus</scene> consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=545143 Biotin Protein Ligase 2008-06-03T13:25:54Z

<p>Nicole R Pendini: </p> <hr /> <div><applet load='1bia' size='500' frame='true' align='right' caption='The first structure of a Biotin Protein Ligase from E.coli' /><br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/1'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <font color="purple"><scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'>The central domain </scene></font> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The C- terminus consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=545142 Biotin Protein Ligase 2008-06-03T13:24:52Z

<p>Nicole R Pendini: </p> <hr /> <div><applet load='1bia' size='500' frame='true' align='right' caption='The first structure of a Biotin Protein Ligase from E.coli' /><br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/1'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. <scene name='Biotin_Protein_Ligase/Apo_ecbpl_cat/1'><font color="purple">The central domain </font></scene> consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The C- terminus consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=545131 Biotin Protein Ligase 2008-06-03T13:15:51Z

<p>Nicole R Pendini: </p> <hr /> <div><applet load='1bia' size='500' frame='true' align='right' caption='The first structure of a Biotin Protein Ligase from E.coli' /><br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The <scene name='Biotin_Protein_Ligase/Apo_ecbpl_nterm/1'>N-terminal</scene> 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. The central domain consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The C- terminus consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=545094 Biotin Protein Ligase 2008-06-03T13:01:27Z

<p>Nicole R Pendini: </p> <hr /> <div><applet load='1bia' size='500' frame='true' align='right' caption='The first structure of a Biotin Protein Ligase from E.coli' /><br /> <br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The N-terminal 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. The central domain consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The C- terminus consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=545093 Biotin Protein Ligase 2008-06-03T12:59:11Z

<p>Nicole R Pendini: </p> <hr /> <div>The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.<br /> <br /> BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, <scene name='Biotin_Protein_Ligase/Apo_ecbpl/1'>apo_EcBPL</scene> . The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The N-terminal 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. The central domain consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The C- terminus consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=545076 Biotin Protein Ligase 2008-06-03T12:50:32Z

<p>Nicole R Pendini: </p> <hr /> <div><br /> The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme. Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.</div>

Nicole R Pendini https://proteopedia.org/index.php?title=Biotin_Protein_Ligase&diff=545065 Biotin Protein Ligase 2008-06-03T12:45:22Z

<p>Nicole R Pendini: New page: Biotin Protein Ligase</p> <hr /> <div>Biotin Protein Ligase</div>

Nicole R Pendini