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https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Jon+Waller Proteopedia - User contributions [en] 2026-09-16T11:05:54Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=User:Jon_Waller&diff=1859844 User:Jon Waller 2013-11-05T23:27:55Z

<p>Jon Waller: </p> <hr /> <div>I graduated with a BSc Biochemistry and Molecular Biology form the University of Northern British Columbia in 2012 and am currently a student in the Faculty of Pharmaceutical Sciences at UBC.</div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_reserved_330&diff=1224516 Sandbox reserved 330 2011-04-03T23:02:35Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_1ne8| PDB=1ne8 | SCENE= }}<br /> <br /> == Background Information==<br /> Addiction modules, consisting of a toxin and antitoxin pair, are controlled by operons which, are autoregulated at the transcriptional level. Bacteria rely on addiction modules to maintain plasmids within populations, and cells that do not inherit the plasmid encoded operon will not produce antixoin and will be inhibited by the toxin via post segregational killing. Once this operon is expressed, the bacterial strain is addicted to the antitoxin for survival. It is known that genomes of most bacteria have a toxin-antitoxin loci, which have been shown to be induced by stressful conditions. So thus, these modules play an important role in plasmid partitioning and cellular response to stress, where the maintenance of these modules prevents the lethal effect of toxin on cells. <br /> <br /> Previous studies of toxin families include MazF, ChpAK, and PemK, which all code for endoribonuclease that activates cellular mRNAs by cleaving them at specific sites. Recently, there is a Bacilis subtilis gene product discovered, EndoA, that is a member of RNAses, which is likely the gene product of the YdcE gene. This EndoA has similar cleavage pattern specificity as MazF and PemK, with cleavage products of a 3’phosphate and 5’OH group. Further study revealed that a coexpression of an upstream gene, YdcD reverses the effects of this particular toxin, and thus, this is the first antitoxin-toxin system of Bacilis subtilis. <br /> <br /> <br /> ==Tautomerase Superfamily==<br /> <br /> The YdcE protein(EndoA) has been categorized as part of a subfamily of the tautomerase superfamily, which includes the 4-oxalocrotonate tautomerase. This superfamily is composed of structurally homologous proteins that are constructed from a simple β-α-β fold. These homologous proteins share a key mechanistic feature of using an amino terminal proline, which has an unsually low pKa, as a general base in a keto-enol tautomerization. <br /> <br /> ==Structure==<br /> <br /> <scene name='Sandbox_reserved_330/Charged_amino_acids/1'>YdcE protein backbone</scene><br /> <br /> Crystallization of the YdcE gene product revealed a crystal with space group of P6522, where a= 56.63, b=56.63, and c=138.257. The final structure model of the YdcE protein was determined to be 2.1 A with an R-factor of 15.9%. The YdcE protein consists of 117 amino acids and is approximately 14 kDa. It is a compact single domain alpha/beta protein, with 3 α helices and 7 β strands. Five out of seven beta strands, β1, β2, β3, β6, and β7 forms an antiparallel sheet. While two of the remaining strands, β4, β5, and C terminus (containing Asp115) of the β3 strand forms a smaller sheet. <br /> <br /> The structure itself is a dimer interface between monomers that is related by a two fold axis, and it exists as a dimer in solution as well. The dimer is a convex surface with a flat surface that includes 3 α helix that has C-terminal tails protruding. The convex surface is an extensive hydrophobic surface between the two monomers, and include Ile 30, Ile 43, Ile 111, Leu 107, Ile 80 and Ile 114. Each monomer has a β6 strand that is paired with each other through hydrogen bonds between the amide of the Thr82 and the carbonyl oxygen of Ile 80. On the convex side of the dimer, hydrogen bonds exist between amides of Ser 19, to the side chain of Asp 84, along with salt bridges between Glu 20 and Arg 87. Between these salt bridges, the Arg 81 of each monomer are buried in the dimer interface and is stabilized by water-mediated hydrogen bonds. Other dimer interactions of the YdcE protein include a hydrogen bond between carbonyl oxygen of Ser 110 and the amide of Asn 32, and between the carbonyl oxygen of Ala 112 and NE of Arg5. <br /> <br /> The YcdE protein has similar structures to other proteins, such as Pem/Kid from E.coli in plasmid R1, and CcdB from E.coli in plasmid F. These similarities include a five stranded antiparallel sheet and a smaller three stranded β-sheet with a C-terminal α helix. YdcE shares 27% sequence similarity with Pem/Kid and 7% with CcdB. However, the electronegative surface potential of YdcE is more negative than Kid and CcdB, with a pI of 4.7. This is largely due to having six charged amino acids; Asp 96, Asp 97, Glu 98, Glu 105, Asp 101, and Asp 104.<br /> [[Image:6_charged_AA.jpg | thumb | right | 300px |6 charged amino acids]]<br /> <br /> ==Active Site==<br /> <br /> Complexes of YdcE reveal that the two active sites of the enzyme are located peripherally at the dimer interface, and are shown to be composed of residues contributed from both monomers of the dimer. The two active sites of the native YdcE protein structure have a few differences to those when complexed with other proteins, however, the largest difference is in the repositioning of the aromatic ring of the Phe8, which is rotated approximately by 32° in the complex structure relative to the native YdcE protein. <br /> <br /> The active site of the YdcE protein is composed of residues from both monomers, with key active site residues consisting of Pro1, Arg 11, Arg 38, Phe50. Dimerization of the two monomers include Pro1, which is presumed to be the catalytic base and is from one subunit, while Phe8, Arg 10, Trp 51, and Tyr72 are from the other monomer. <br /> <br /> ==Conclusion==<br /> The Bacilis subtilis YdcE gene encodes an endoribonuclease called EndoA, which is a member of the MazF/PemK family of bacterial toxin and the protein encoded by the gene YdcD is an inhibitor of its activity. EndoA cleaves in a UAC sequence, which is predicted to be a single stranded conformation, and has an overlapping cleavage site specificity with the E.coli homologues. EndoA activity results in cleavage products with a 3’phosphate and 5’OH group, which is typical of degradative RNAses that functions in the absence of divalent cations. <br /> <br /> <ref>PMID:14517982</ref><br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=File:6_charged_AA.jpg&diff=1224515 File:6 charged AA.jpg 2011-04-03T23:01:38Z

<p>Jon Waller: </p> <hr /> <div></div>

Jon Waller https://proteopedia.org/index.php?title=Porphobilinogen_Deaminase&diff=1220196 Porphobilinogen Deaminase 2011-03-29T02:07:07Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. DPM consists of two pyrole units disulfide-bound to CYS[242]<ref > A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Mechanism==<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 2025226</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD<ref name="Lander">PMID: 2025226</ref>. The six pyrole unit compound is cleaved at the second pyrole, by water, to yield the final product, hydroxymethylbilane<ref> A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. <br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> Acute intermittent porphyria (AIP) is an autosomal dominant disorder (0.06% incidence rate in population) caused by a mutation in the hydroxymethylbilane synthase gene (HMBS)<ref name="Whatley">Whatley S.D., Roberts A.G., Llewellyn D.H., Bennett C.P., Garrett C, Elder G.H. (2000). Non-erythroid form of acute intermittent porphyria caused by promoter and frameshift mutations distant from the coding sequence of exon 1 of the HMBS gene. Hum. Genet. 107 (3): 243–248.</ref>. The protein, responsible for the conversion of porphobilinogen (PBG) to hydroxymethylbilane (HMB) is less active in most affected individuals by approximately one-half normal activity<ref name="Whatley" />. Defective PBGD, AIP, and can be diagnosed through the detection of increased concentrations of porphobilinogen (PBG) in urine as it remains unincorporated by the defective enzyme<ref name="Aarsand">PMID: 16595824</ref>.<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Porphobilinogen_Deaminase&diff=1220195 Porphobilinogen Deaminase 2011-03-29T02:06:38Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. DPM consists of two pyrole units disulfide-bound to CYS[242]<ref > A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Mechanism==<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 2025226</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD<ref name="Lander">PMID: 2025226</ref>. The six pyrole unit compound is cleaved at the second pyrole, by water, to yield the final product, hydroxymethylbilane<ref> A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. <br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> Acute intermittent porphyria (AIP) is an autosomal dominant disorder (0.06% incidence rate in population) caused by a mutation in the hydroxymethylbilane synthase gene (HMBS)<ref name="Whatley">Whatley S.D., Roberts A.G., Llewellyn D.H., Bennett C.P., Garrett C, Elder G.H. (2000). Non-erythroid form of acute intermittent porphyria caused by promoter and frameshift mutations distant from the coding sequence of exon 1 of the HMBS gene. Hum. Genet. 107 (3): 243–248.</ref>. The protein, responsible for the conversion of porphobilinogen (PBG) to hydroxymethylbilane (HMB) is less active in most affected individuals by approximately one-half normal activity<ref name="Whatley" />. Defective PBGD, AIP, and can be diagnosed through the detection of increased concentrations of porphobilinogen (PBG) in urine as it remains unincorporated by the defective enzyme<ref name="Aarsand">PMID: 16595824</ref>.<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1220193 Sandbox Reserved 349 2011-03-29T02:05:16Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. DPM consists of two pyrole units disulfide-bound to CYS[242]<ref > A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Mechanism==<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 2025226</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD<ref name="Lander">PMID: 2025226</ref>. The six pyrole unit compound is cleaved at the second pyrole, by water, to yield the final product, hydroxymethylbilane<ref> A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. <br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> Acute intermittent porphyria (AIP) is an autosomal dominant disorder (0.06% incidence rate in population) caused by a mutation in the hydroxymethylbilane synthase gene (HMBS)<ref name="Whatley">Whatley S.D., Roberts A.G., Llewellyn D.H., Bennett C.P., Garrett C, Elder G.H. (2000). Non-erythroid form of acute intermittent porphyria caused by promoter and frameshift mutations distant from the coding sequence of exon 1 of the HMBS gene. Hum. Genet. 107 (3): 243–248.</ref>. The protein, responsible for the conversion of porphobilinogen (PBG) to hydroxymethylbilane (HMB) is less active in most affected individuals by approximately one-half normal activity<ref name="Whatley" />. Defective PBGD, AIP, and can be diagnosed through the detection of increased concentrations of porphobilinogen (PBG) in urine as it remains unincorporated by the defective enzyme<ref name="Aarsand">PMID: 16595824</ref>.<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1220192 Sandbox Reserved 349 2011-03-29T02:04:19Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. DPM consists of two pyrole units disulfide-bound to CYS[242]<ref > A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Mechanism==<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 2025226</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD<ref name="Lander">PMID: 2025226</ref>. The six pyrole unit compound is cleaved at the second pyrole, by water, to yield the final product, hydroxymethylbilane<ref> A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. <br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> Acute intermittent porphyria (AIP) is an autosomal dominant disorder (0.06% incidence rate in population) caused by a mutation in the hydroxymethylbilane synthase gene (HMBS)<ref name="Whatley">Whatley S.D., Roberts A.G., Llewellyn D.H., Bennett C.P., Garrett C, Elder G.H. (2000). Non-erythroid form of acute intermittent porphyria caused by promoter and frameshift mutations distant from the coding sequence of exon 1 of the HMBS gene. Hum. Genet. 107 (3): 243–248.</ref>. The protein, responsible for the conversion of porphobilinogen (PBG) to hydroxymethylbilane (HMB) is less active in most affected individuals by approximately one-half normal activity<ref name="Whatley"></ref>. Defective PBGD, AIP, and can be diagnosed through the detection of increased concentrations of porphobilinogen (PBG) in urine as it remains unincorporated by the defective enzyme<ref name="Aarsand">PMID: 16595824</ref>.<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1220191 Sandbox Reserved 349 2011-03-29T02:03:04Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. DPM consists of two pyrole units disulfide-bound to CYS[242]<ref > A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Mechanism==<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 2025226</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD<ref name="Lander">PMID: 2025226</ref>. The six pyrole unit compound is cleaved at the second pyrole, by water, to yield the final product, hydroxymethylbilane<ref> A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. <br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> Acute intermittent porphyria (AIP) is an autosomal dominant disorder (0.06% incidence rate in population) caused by a mutation in the hydroxymethylbilane synthase gene (HMBS)<ref name="Whatley">Whatley S.D., Roberts A.G., Llewellyn D.H., Bennett C.P., Garrett C, Elder G.H. (2000). Non-erythroid form of acute intermittent porphyria caused by promoter and frameshift mutations distant from the coding sequence of exon 1 of the HMBS gene. Hum. Genet. 107 (3): 243–248.</ref>. The protein, responsible for the conversion of porphobilinogen (PBG) to hydroxymethylbilane (HMB) is less active in most affected individuals by approximately one-half normal activity<ref name="Whatley"name="Whatley"></ref>. Defective PBGD, AIP, and can be diagnosed through the detection of increased concentrations of porphobilinogen (PBG) in urine as it remains unincorporated by the defective enzyme<ref name="Aarsand">PMID: 16595824</ref>.<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1220190 Sandbox Reserved 349 2011-03-29T02:01:04Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. DPM consists of two pyrole units disulfide-bound to CYS[242]<ref > A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Mechanism==<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 2025226</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD<ref name="Lander">PMID: 2025226</ref>. The six pyrole unit compound is cleaved at the second pyrole, by water, to yield the final product, hydroxymethylbilane<ref> A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. <br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> Acute intermittent porphyria (AIP) is an autosomal dominant disorder (0.06% incidence rate in population) caused by a mutation in the hydroxymethylbilane synthase gene (HMBS)<ref>Whatley S.D., Roberts A.G., Llewellyn D.H., Bennett C.P., Garrett C, Elder G.H. (2000). Non-erythroid form of acute intermittent porphyria caused by promoter and frameshift mutations distant from the coding sequence of exon 1 of the HMBS gene. Hum. Genet. 107 (3): 243–248.</ref>. The protein, responsible for the conversion of porphobilinogen (PBG) to hydroxymethylbilane (HMB) is less active in most affected individuals by approximately one-half normal activity<ref>Whatley S.D., Roberts A.G., Llewellyn D.H., Bennett C.P., Garrett C, Elder G.H. (2000). Non-erythroid form of acute intermittent porphyria caused by promoter and frameshift mutations distant from the coding sequence of exon 1 of the HMBS gene. Hum. Genet. 107 (3): 243–248.</ref>. Defective PBGD, AIP, and can be diagnosed through the detection of increased concentrations of porphobilinogen (PBG) in urine as it remains unincorporated by the defective enzyme<ref name="Aarsand">PMID: 16595824</ref>.<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1220189 Sandbox Reserved 349 2011-03-29T01:56:23Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. DPM consists of two pyrole units disulfide-bound to CYS[242]<ref > A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Mechanism==<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 2025226</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD<ref name="Lander">PMID: 2025226</ref>. The six pyrole unit compound is cleaved at the second pyrole, by water, to yield the final product, hydroxymethylbilane<ref> A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. <br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> Acute intermittent porphyria (AIP) is an autosomal dominant disorder (0.06% incidence rate in population) caused by a mutation in the hydroxymethylbilane synthase gene (HMBS)<ref name="Whatley">PMID:11071386</ref>. The protein, responsible for the conversion of porphobilinogen (PBG) to hydroxymethylbilane (HMB) is less active in most affected individuals by approximately one-half normal activity<ref name="Whatley">PMID:11071386</ref>. Defective PBGD, AIP, and can be diagnosed through the detection of increased concentrations of porphobilinogen (PBG) in urine as it remains unincorporated by the defective enzyme<ref name="Aarsand">PMID: 16595824</ref>.<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1220184 Sandbox Reserved 349 2011-03-29T01:42:20Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. DPM consists of two pyrole units disulfide-bound to CYS[242]<ref > A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Mechanism==<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 2025226</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD<ref name="Lander">PMID: 2025226</ref>. The six pyrole unit compound is cleaved at the second pyrole to yield the final product, hydroxymethylbilane<ref> A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. <br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> <br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1220182 Sandbox Reserved 349 2011-03-29T01:38:39Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. DPM consists of two pyrole units disulfide-bound to CYS[242]<ref > A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Mechanism==<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 2025226</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD<ref name="Lander">PMID: 2025226</ref>. <br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> <br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1220172 Sandbox Reserved 349 2011-03-29T01:10:22Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ===Mechanism===<br /> ==Importance of hPBGD==<br /> ===Acute Intermittent Porphyria===<br /> PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits<ref name="Peter">PMID:3079571</ref>. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor<ref name="Lander">PMID: 1150073</ref>. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor<ref name="Lander">PMID: 1150073</ref>.<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1216089 Sandbox Reserved 349 2011-03-16T17:05:45Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ===Mechanism===<br /> <br /> ===Acute Intermittent Porphyria===<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1216085 Sandbox Reserved 349 2011-03-16T17:01:19Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ===Mechanism===<br /> <br /> ===Acute Intermittent Porphyria===<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1216082 Sandbox Reserved 349 2011-03-16T16:57:31Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/3' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm/3'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ===Mechanism===<br /> <br /> ===Acute Intermittent Porphyria===<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1201215 Sandbox Reserved 349 2011-03-07T21:42:44Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='250' frame='true' align='left' scene='Sandbox_Reserved_349/Dpm/2' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ===Mechanism===<br /> <br /> ===Acute Intermittent Porphyria===<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1201213 Sandbox Reserved 349 2011-03-07T21:40:43Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='300' frame='true' align='left' caption='Dipyrromethane in the active site' scene='Sandbox_Reserved_349/Dpm/2' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Function==<br /> ===Mechanism===<br /> <br /> ===Acute Intermittent Porphyria===<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1200562 Sandbox Reserved 349 2011-03-03T02:52:44Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='300' frame='true' align='left' caption='Dipyrromethane in the active site' scene='Sandbox_Reserved_349/Dpm/2' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> <br /> ==Function==<br /> ===Mechanism===<br /> <br /> ===Acute Intermittent Porphyria===<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1200538 Sandbox Reserved 349 2011-03-03T02:42:30Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='300' frame='true' align='left' caption='Dipyrromethane in the active site' scene='Sandbox_Reserved_349/Dpm/2' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ====Mechanism====<br /> <br /> ====Acute Intermittent Porphyria====<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1200535 Sandbox Reserved 349 2011-03-03T02:40:50Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='300' frame='true' align='left' caption='Dipyrromethane in the active site' scene='Sandbox_Reserved_349/Dpm/2' /><br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> <br /> <br /> ==Function==<br /> ====Mechanism====<br /> <br /> ====Acute Intermittent Porphyria====<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1200534 Sandbox Reserved 349 2011-03-03T02:40:18Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='300' frame='true' align='left' caption='Dipyrromethane in the active site' scene='Sandbox_Reserved_349/Dpm/2' /><br /> <br /> <br /> <br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ====Mechanism====<br /> <br /> ====Acute Intermittent Porphyria====<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1200524 Sandbox Reserved 349 2011-03-03T02:32:33Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> <Structure load='3eq1' size='300' frame='true' align='left' caption='Dipyrromethane in the active site' scene='Sandbox_Reserved_349/Dpm/2' /><br /> <br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ====Mechanism====<br /> <br /> ====Acute Intermittent Porphyria====<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1200506 Sandbox Reserved 349 2011-03-03T02:22:09Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ===Mechanism===<br /> <br /> ===Acute Intermittent Porphyria===<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1200503 Sandbox Reserved 349 2011-03-03T02:20:22Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ===Sub1===<br /> :This mechanism on the formation of hydroxymethylbilane by porphobilinogen deaminase is modelled based on the research of Lander ''et al.''1992<ref name="Lander">PMID: 1150073</ref>.<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1200497 Sandbox Reserved 349 2011-03-03T02:16:28Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> __TOC__<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'''Mechanism'''<br /> :This mechanism on the formation of hydroxymethylbilane by porphobilinogen deaminase is modelled based on the research of Lander ''et al.''1992<ref name="Lander">PMID: 1150073</ref>.<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1200412 Sandbox Reserved 349 2011-03-02T08:37:22Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/So4_hbond/1'>sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'''Mechanism'''<br /> :This mechanism on the formation of hydroxymethylbilane by porphobilinogen deaminase is modelled based on the research of Lander ''et al.''1992<ref name="Lander">PMID: 1150073</ref>.<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198696 Sandbox Reserved 349 2011-03-01T19:19:29Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'''Mechanism'''<br /> :This mechanism on the formation of hydroxymethylbilane by porphobilinogen deaminase is modelled based on the research of Lander ''et al.''1992<ref name="Lander">PMID: 1150073</ref>.<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198695 Sandbox Reserved 349 2011-03-01T19:17:45Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'''Mechanism'''<br /> This mechanism on the formation of hydroxymethylbilane by porphobilinogen deaminase is modelled based on the research of Lander ''et al.''1992<ref name="Lander">PMID: 1150073</ref>.<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198694 Sandbox Reserved 349 2011-03-01T19:14:50Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'''Mechanism'''<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198693 Sandbox Reserved 349 2011-03-01T19:14:15Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;====='''Mechanism'''=====<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198692 Sandbox Reserved 349 2011-03-01T19:13:35Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ====='''Mechanism'''=====<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198691 Sandbox Reserved 349 2011-03-01T19:12:43Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ====='''Mechanism'''=====<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198690 Sandbox Reserved 349 2011-03-01T19:12:18Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function====<br /> ==='''Mechanism'''=====<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198689 Sandbox Reserved 349 2011-03-01T19:11:57Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ==='''Mechanism'''===<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198688 Sandbox Reserved 349 2011-03-01T18:52:58Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198687 Sandbox Reserved 349 2011-03-01T18:47:42Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids; the human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198686 Sandbox Reserved 349 2011-03-01T18:46:37Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids; the human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domain three while ''E.coli'' PBGD is lacking this extended loop <ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198622 Sandbox Reserved 349 2011-02-28T23:19:48Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198621 Sandbox Reserved 349 2011-02-28T23:15:56Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/2'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered <scene name='Sandbox_Reserved_349/Sulfate_and_serarg/1'>Sulfate ions</scene> are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enyme<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198617 Sandbox Reserved 349 2011-02-28T22:18:14Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> ==Structure==<br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enyme<ref name="Raj">PMID: 19207107</ref>.<br /> ==Function==<br /> ==Importance of hPBGD==<br /> ==References==<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198616 Sandbox Reserved 349 2011-02-28T22:17:41Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD (hPBGD) gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> =Structure= <br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enyme<ref name="Raj">PMID: 19207107</ref>.<br /> =Function=<br /> =Importance of hPBGD=<br /> =References=<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198615 Sandbox Reserved 349 2011-02-28T22:14:04Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> =Structure= <br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enyme<ref name="Raj">PMID: 19207107</ref>.<br /> =Function=<br /> <br /> =References=<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198614 Sandbox Reserved 349 2011-02-28T22:13:28Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> =General Information=<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> =Structure= <br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enyme<ref name="Raj">PMID: 19207107</ref>.<br /> =Function=<br /> <br /> =References=<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198613 Sandbox Reserved 349 2011-02-28T22:12:28Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Porphobilinogen deaminase=<br /> =Structure= <br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enyme<ref name="Raj">PMID: 19207107</ref>.<br /> =Function=<br /> <br /> =References=<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198612 Sandbox Reserved 349 2011-02-28T22:11:46Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> ="'Porphobilinogen deaminase"'=<br /> =Structure= <br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enyme<ref name="Raj">PMID: 19207107</ref>.<br /> =Function=<br /> <br /> =References=<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198611 Sandbox Reserved 349 2011-02-28T22:11:06Z

<p>Jon Waller: </p> <hr /> <div>{{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> <br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Structure= <br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enyme<ref name="Raj">PMID: 19207107</ref>.<br /> =Function=<br /> <br /> =References=<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198610 Sandbox Reserved 349 2011-02-28T22:10:06Z

<p>Jon Waller: </p> <hr /> <div>='''Porphobilinogen Deaminase'''=<br /> {{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Structure= <br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%<ref name="Raj">PMID: 19207107</ref>. Therefore, it is generally assumed that this protein is active naturally as a monomeric enyme<ref name="Raj">PMID: 19207107</ref>.<br /> =Function=<br /> <br /> =References=<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198609 Sandbox Reserved 349 2011-02-28T22:06:06Z

<p>Jon Waller: </p> <hr /> <div>='''Porphobilinogen Deaminase'''=<br /> {{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a dimeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Structure= <br /> Human PBGD is a three-domain polypeptide with each domain consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. In the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> =Function=<br /> <br /> =References=<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller https://proteopedia.org/index.php?title=Sandbox_Reserved_349&diff=1198608 Sandbox Reserved 349 2011-02-28T22:03:57Z

<p>Jon Waller: </p> <hr /> <div>='''Porphobilinogen Deaminase'''=<br /> {{STRUCTURE_3eq1 | PDB=3eq1 | SCENE= }}<br /> Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a dimeric polypeptide and is the third enzyme in the heme biosynthesis pathways in mammals<ref name="Raj">PMID: 19207107</ref>. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of [[Porphyrin]]<ref name="Peter">PMID:3079571</ref>. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes<ref name="Anderson">PMID:7354069</ref>. <scene name='Sandbox_Reserved_349/Dpm/1'>Dipyrromethane (DPM)</scene>, a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains<ref name="Peter">PMID:3079571</ref>. Mutations in the human PBGD gene are responsible for the condition Acute Intermittent Porphyria (AIP) in humans<ref name="Raj">PMID: 19207107</ref>.<br /> =Structure=<br /> The human PBGD is three domain polypeptide each consisting of approximately 110 amino acids<ref name="Raj">PMID: 19207107</ref>. in the active site, a unique molecule known as <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene><br /> <scene name='Template:Sandbox_Reserved_349/Dpm_site/2'>Dipyrromethane</scene> interacts with porphobilinogen and anchors it in place<ref name="Raj">PMID: 19207107</ref>. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues that are highly conserved amongst human and ''E.coli'' variants of PBGD<ref name="Raj">PMID: 19207107</ref>.<br /> =Function=<br /> <br /> =References=<br /> <references/><br /> <scene name='Sandbox_Reserved_349/Dpm/1'>TextToBeDisplayed</scene></div>

Jon Waller