3eq1

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{{Seed}}
 
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[[Image:3eq1.jpg|left|200px]]
 
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==The Crystal Structure of Human Porphobilinogen Deaminase at 2.8A resolution==
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The line below this paragraph, containing "STRUCTURE_3eq1", creates the "Structure Box" on the page.
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<StructureSection load='3eq1' size='340' side='right'caption='[[3eq1]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3eq1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EQ1 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_3eq1| PDB=3eq1 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3eq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eq1 OCA], [https://pdbe.org/3eq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eq1 RCSB], [https://www.ebi.ac.uk/pdbsum/3eq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eq1 ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/HEM3_HUMAN HEM3_HUMAN] Defects in HMBS are the cause of acute intermittent porphyria (AIP) [MIM:[https://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>
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== Function ==
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[https://www.uniprot.org/uniprot/HEM3_HUMAN HEM3_HUMAN] Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eq/3eq1_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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/main_output.php?pdb_ID=3eq1 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Mutations in the human PBGD (porphobilinogen deaminase) gene cause the inherited defect AIP (acute intermittent porphyria). In the present study we report the structure of the human uPBGD (ubiquitous PBGD) mutant, R167Q, that has been determined by X-ray crystallography and refined to 2.8 A (1 A=0.1 nm) resolution (Rfactor=0.26, Rfree=0.29). The protein crystallized in space group P2(1)2(1)2 with two molecules in the asymmetric unit (a=81.0 A, b=104.4 A and c=109.7 A). Phases were obtained by molecular replacement using the Escherichia coli PBGD structure as a search model. The human enzyme is composed of three domains each of approx. 110 amino acids and possesses a dipyrromethane cofactor at the active site, which is located between domains 1 and 2. An ordered sulfate ion is hydrogen-bonded to Arg26 and Ser28 at the proposed substrate-binding site in domain 1. An insert of 29 amino acid residues, present only in mammalian PBGD enzymes, has been modelled into domain 3 where it extends helix alpha2(3) and forms a beta-hairpin structure that contributes to a continuous hydrogen-bonding network spanning domains 1 and 3. The structural and functional implications of the R167Q mutation and other mutations that result in AIP are discussed.
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===The Crystal Structure of Human Porphobilinogen Deaminase at 2.8A resolution===
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Structure of human porphobilinogen deaminase at 2.8 A: the molecular basis of acute intermittent porphyria.,Gill R, Kolstoe SE, Mohammed F, Al D-Bass A, Mosely JE, Sarwar M, Cooper JB, Wood SP, Shoolingin-Jordan PM Biochem J. 2009 Apr 28;420(1):17-25. PMID:19207107<ref>PMID:19207107</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3eq1" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19207107}}, adds the Publication Abstract to the page
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*[[Porphobilinogen Deaminase|Porphobilinogen Deaminase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19207107 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19207107}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3EQ1 is a 2 chains structure of sequences 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=3EQ1 OCA].
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==Reference==
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<ref group="xtra">PMID:19207107</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Hydroxymethylbilane synthase]]
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[[Category: Large Structures]]
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[[Category: Gill, R.]]
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[[Category: Gill R]]
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[[Category: Kolstoe, S E.]]
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[[Category: Kolstoe SE]]
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[[Category: Mohammed, F.]]
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[[Category: Mohammed F]]
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[[Category: Wood, S P.]]
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[[Category: Wood SP]]
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[[Category: Alpha and beta protein]]
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[[Category: Alternative splicing]]
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[[Category: Cytoplasm]]
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[[Category: Disease mutation]]
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[[Category: Heme biosynthesis]]
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[[Category: Porphyrin biosynthesis]]
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[[Category: Transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 4 14:50:42 2009''
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Current revision

The Crystal Structure of Human Porphobilinogen Deaminase at 2.8A resolution

PDB ID 3eq1

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