3ecr: Difference between revisions
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==Structure of human porphobilinogen deaminase== | |||
=== | <StructureSection load='3ecr' size='340' side='right' caption='[[3ecr]], [[Resolution|resolution]] 2.18Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ecr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ECR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ECR FirstGlance]. <br> | |||
==Disease== | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPM:3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC+ACID'>DPM</scene></td></tr> | ||
[[http://www.uniprot.org/uniprot/HEM3_HUMAN HEM3_HUMAN]] Defects in HMBS are the cause of acute intermittent porphyria (AIP) [MIM:[http://omim.org/entry/176000 176000]]. AIP is a form of porphyria. Porphyrias are inherited defects in the biosynthesis of heme, resulting in the accumulation and increased excretion of porphyrins or porphyrin precursors. They are classified as erythropoietic or hepatic, depending on whether the enzyme deficiency occurs in red blood cells or in the liver. AIP is an autosomal dominant form of hepatic porphyria characterized by acute attacks of neurological dysfunctions with abdominal pain, hypertension, tachycardia, and peripheral neuropathy. Most attacks are precipitated by drugs, alcohol, caloric deprivation, infections, or endocrine factors.<ref>PMID:2243128</ref><ref>PMID:1714233</ref><ref>PMID:1496994</ref><ref>PMID:1427766</ref><ref>PMID:1301948</ref><ref>PMID:8262523</ref><ref>PMID:8401516</ref><ref>PMID:8268934</ref><ref>PMID:8270254</ref><ref>PMID:8270256</ref><ref>PMID:8081367</ref><ref>PMID:7962538</ref><ref>PMID:7757070</ref><ref>PMID:8825929</ref><ref>PMID:9199558</ref><ref>PMID:9225970</ref><ref>PMID:9654202</ref><ref>PMID:9463797</ref><ref>PMID:10494093</ref><ref>PMID:10453740</ref><ref>PMID:10502788</ref><ref>PMID:10657149</ref><ref>PMID:10602775</ref><ref>PMID:11399210</ref><ref>PMID:11030413</ref><ref>PMID:10782018</ref><ref>PMID:11013452</ref>[:]<ref>PMID:12406973</ref><ref>PMID:12372055</ref><ref>PMID:11857754</ref><ref>PMID:14669009</ref><ref>PMID:14970743</ref><ref>PMID:15669678</ref> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HMBS, PBGD, UPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxymethylbilane_synthase Hydroxymethylbilane synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.61 2.5.1.61] </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=3ecr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ecr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ecr RCSB], [http://www.ebi.ac.uk/pdbsum/3ecr PDBsum]</span></td></tr> | |||
</table> | |||
== Disease == | |||
[[http://www.uniprot.org/uniprot/HEM3_HUMAN HEM3_HUMAN]] Defects in HMBS are the cause of acute intermittent porphyria (AIP) [MIM:[http://omim.org/entry/176000 176000]]. AIP is a form of porphyria. Porphyrias are inherited defects in the biosynthesis of heme, resulting in the accumulation and increased excretion of porphyrins or porphyrin precursors. They are classified as erythropoietic or hepatic, depending on whether the enzyme deficiency occurs in red blood cells or in the liver. AIP is an autosomal dominant form of hepatic porphyria characterized by acute attacks of neurological dysfunctions with abdominal pain, hypertension, tachycardia, and peripheral neuropathy. Most attacks are precipitated by drugs, alcohol, caloric deprivation, infections, or endocrine factors.<ref>PMID:2243128</ref> <ref>PMID:1714233</ref> <ref>PMID:1496994</ref> <ref>PMID:1427766</ref> <ref>PMID:1301948</ref> <ref>PMID:8262523</ref> <ref>PMID:8401516</ref> <ref>PMID:8268934</ref> <ref>PMID:8270254</ref> <ref>PMID:8270256</ref> <ref>PMID:8081367</ref> <ref>PMID:7962538</ref> <ref>PMID:7757070</ref> <ref>PMID:8825929</ref> <ref>PMID:9199558</ref> <ref>PMID:9225970</ref> <ref>PMID:9654202</ref> <ref>PMID:9463797</ref> <ref>PMID:10494093</ref> <ref>PMID:10453740</ref> <ref>PMID:10502788</ref> <ref>PMID:10657149</ref> <ref>PMID:10602775</ref> <ref>PMID:11399210</ref> <ref>PMID:11030413</ref> <ref>PMID:10782018</ref> <ref>PMID:11013452</ref> [:]<ref>PMID:12406973</ref> <ref>PMID:12372055</ref> <ref>PMID:11857754</ref> <ref>PMID:14669009</ref> <ref>PMID:14970743</ref> <ref>PMID:15669678</ref> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/HEM3_HUMAN HEM3_HUMAN]] Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. | |||
== 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/ec/3ecr_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Acute intermittent porphyria (AIP), an inherited disease of heme biosynthesis, is one of the most common types of porphyria. Reduced activity of the enzyme porphobilinogen deaminase (PBGD), which catalyzes the sequential condensation of 4 molecules of porphobilinogen to yield preuroporphyrinogen, has been linked to the symptoms of AIP. We have determined the 3-dimensional structure of human PBGD at 2.2 A resolution. Analysis of the structure revealed a dipyrromethane cofactor molecule covalently linked to C261, sitting in a positively charged cleft region. In addition to the critical catalytic D99, a number of other residues are seen hydrogen bonded to the cofactor and play a role in catalysis. Sequential entry of 4 pyrrole molecules into the active site is accomplished by movement of the domains around the hinges. H120P mutation resulted in an inactive enzyme, supporting the role of H120 as a hinge residue. Interestingly, some of the mutations of the human PBGD documented in patients suffering from AIP are located far away from the active site. The structure provides insights into the mechanism of action of PBGD at the molecular level and could aid the development of potential drugs for the up-regulation of PBGD activity in AIP. | |||
Structural insight into acute intermittent porphyria.,Song G, Li Y, Cheng C, Zhao Y, Gao A, Zhang R, Joachimiak A, Shaw N, Liu ZJ FASEB J. 2009 Feb;23(2):396-404. Epub 2008 Oct 20. PMID:18936296<ref>PMID:18936296</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Porphobilinogen Deaminase|Porphobilinogen Deaminase]] | *[[Porphobilinogen Deaminase|Porphobilinogen Deaminase]] | ||
== References == | |||
== | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Hydroxymethylbilane synthase]] | [[Category: Hydroxymethylbilane synthase]] | ||
[[Category: Cheng, C | [[Category: Cheng, C]] | ||
[[Category: Gao, A | [[Category: Gao, A]] | ||
[[Category: Joachimiak, A | [[Category: Joachimiak, A]] | ||
[[Category: Li, Y | [[Category: Li, Y]] | ||
[[Category: Liu, Z J | [[Category: Liu, Z J]] | ||
[[Category: Shaw, N | [[Category: Shaw, N]] | ||
[[Category: Song, G | [[Category: Song, G]] | ||
[[Category: Zhang, R | [[Category: Zhang, R]] | ||
[[Category: Zhao, Y | [[Category: Zhao, Y]] | ||
[[Category: Disease mutation]] | [[Category: Disease mutation]] | ||
[[Category: Heme biosynthesis]] | [[Category: Heme biosynthesis]] |
Revision as of 17:06, 18 December 2014
Structure of human porphobilinogen deaminaseStructure of human porphobilinogen deaminase
Structural highlights
Disease[HEM3_HUMAN] Defects in HMBS are the cause of acute intermittent porphyria (AIP) [MIM:176000]. AIP is a form of porphyria. Porphyrias are inherited defects in the biosynthesis of heme, resulting in the accumulation and increased excretion of porphyrins or porphyrin precursors. They are classified as erythropoietic or hepatic, depending on whether the enzyme deficiency occurs in red blood cells or in the liver. AIP is an autosomal dominant form of hepatic porphyria characterized by acute attacks of neurological dysfunctions with abdominal pain, hypertension, tachycardia, and peripheral neuropathy. Most attacks are precipitated by drugs, alcohol, caloric deprivation, infections, or endocrine factors.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [:][28] [29] [30] [31] [32] [33] Function[HEM3_HUMAN] Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. 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 PubMedAcute intermittent porphyria (AIP), an inherited disease of heme biosynthesis, is one of the most common types of porphyria. Reduced activity of the enzyme porphobilinogen deaminase (PBGD), which catalyzes the sequential condensation of 4 molecules of porphobilinogen to yield preuroporphyrinogen, has been linked to the symptoms of AIP. We have determined the 3-dimensional structure of human PBGD at 2.2 A resolution. Analysis of the structure revealed a dipyrromethane cofactor molecule covalently linked to C261, sitting in a positively charged cleft region. In addition to the critical catalytic D99, a number of other residues are seen hydrogen bonded to the cofactor and play a role in catalysis. Sequential entry of 4 pyrrole molecules into the active site is accomplished by movement of the domains around the hinges. H120P mutation resulted in an inactive enzyme, supporting the role of H120 as a hinge residue. Interestingly, some of the mutations of the human PBGD documented in patients suffering from AIP are located far away from the active site. The structure provides insights into the mechanism of action of PBGD at the molecular level and could aid the development of potential drugs for the up-regulation of PBGD activity in AIP. Structural insight into acute intermittent porphyria.,Song G, Li Y, Cheng C, Zhao Y, Gao A, Zhang R, Joachimiak A, Shaw N, Liu ZJ FASEB J. 2009 Feb;23(2):396-404. Epub 2008 Oct 20. PMID:18936296[34] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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