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Crystal structure of human prostacyclin synthase
Biology and Chemistry Report
2IAG
  •   Structure Details   Hide

    Structure Keywords

    Keywords ISOMERASE
    Text prostacyclin synthase, Class III cytochorme P450, hemoprotein, CYP8A1, ISOMERASE

    Polymeric Molecules

    Chain A,B
    Description Prostacyclin synthase 
    Fragment residues 23-500 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 55356.1 
    Source Method genetically manipulated  
    Entity Name Prostaglandin I2 synthase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    HEM  PROTOPORPHYRIN IX CONTAINING FE  C34 H32 Fe N4 O4   616.49  View 
    NA  SODIUM ION  Na   22.99  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B PTGIS_HUMAN Q16647     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  5.3.99.4      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    1516   Prostaglandin Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Prostaglandins Any of a Group of Biologically Active Metabolites Which Contain a Cyclopentane Ring. 
    6629   Lipid Metabolic Process  The Chemical Reactions and Pathways Involving Lipids Compounds Soluble in an Organic Solvent But Not or Sparingly in an Aqueous Solvent. Includes Fatty Acids; Neutral Fats Other Fatty Acid Esters and Soaps; Long Chain (fatty) Alcohols and Waxes; Sphingoids and Other Long Chain Bases; Glycolipids Phospholipids and Sphingolipids; and Carotenes Polyprenols Sterols Terpenes and Other Isoprenoids. 
    6631   Fatty Acid Metabolic Process  The Chemical Reactions and Pathways Involving Fatty Acids Aliphatic Monocarboxylic Acids Liberated From Naturally Occurring Fats and Oils by Hydrolysis. 
    6633   Fatty Acid Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of a Fatty Acid Any of the Aliphatic Monocarboxylic Acids That Can Be Liberated by Hydrolysis From Naturally Occurring Fats and Oils. Fatty Acids Are Predominantly Straight Chain Acids of 4 to 24 Carbon Atoms Which May Be Saturated or Unsaturated; Branched Fatty Acids and Hydroxy Fatty Acids Also Occur and Very Long Chain Acids of Over 30 Carbons Are Found in Waxes. 
    6690   Icosanoid Metabolic Process  The Chemical Reactions and Pathways Involving Icosanoids Any of a Group of C20 Polyunsaturated Fatty Acids. 
    6693   Prostaglandin Metabolic Process  The Chemical Reactions and Pathways Involving Prostaglandins Any of a Group of Biologically Active Metabolites Which Contain a Cyclopentane Ring Due to the Formation of a Bond Between Two Carbons of a Fatty Acid. They Have a Wide Range of Biological Activities. 
    6766   Vitamin Metabolic Process  The Chemical Reactions and Pathways Involving Vitamins. Vitamin Is a General Term For a Number of Unrelated Organic Substances That Occur in Many Foods in Small Amounts and That Are Necessary in Trace Amounts For the Normal Metabolic Functioning of the Body. Vitamins May Be Water Soluble or Fat Soluble and Usually Serve As Components of Coenzyme Systems. 
    6767   Water Soluble Vitamin Metabolic Process  The Chemical Reactions and Pathways Involving Any of a Diverse Group of Vitamins That Are Soluble in Water. 
    6769   Nicotinamide Metabolic Process  The Chemical Reactions and Pathways Involving Nicotinamide Pyridine 3 Carboxamide the Amide of Nicotinic Acid. It Is a Member of the B Complex of Vitamins and Occurs Widely in Living Organisms. 
    6805   Xenobiotic Metabolic Process  The Chemical Reactions and Pathways Involving a Xenobiotic Compound a Compound Foreign to Living Organisms. Used of Chemical Compounds E.g. a Xenobiotic Chemical Such As a Pesticide. 
    19369   Arachidonic Acid Metabolic Process  The Chemical Reactions and Pathways Involving Arachidonic Acid a Straight Chain Fatty Acid with 20 Carbon Atoms and Four Double Bonds Per Molecule. Arachidonic Acid Is the All Z (5 8 11 14) Isomer. 
    19371   Cyclooxygenase Pathway  The Chemical Reactions and Pathways by Which Prostaglandins Are Formed From Arachidonic Acid and in Which Prostaglandin Endoperoxide Synthase (cyclooxygenase) Catalyzes the Committed Step in the Conversion of Arachidonic Acid to the Prostaglandin Endoperoxides Pgg2 and Pgh2. 
    19674   NAD Metabolic Process  The Chemical Reactions and Pathways Involving Nicotinamide Adenine Dinucleotide (nad) a Coenzyme Present in Most Living Cells and Derived From the B Vitamin Nicotinic Acid. 
    32088   Negative Regulation of Nf Kappab Transcription Factor Activity  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of the Activity of the Transcription Factor Nf Kappab. 
    35360   Positive Regulation of Peroxisome Proliferator Activated Receptor Signaling Pathway  Any Process That Activates or Increases the Frequency Rate or Extent of the Peroxisome Proliferator Activated Receptor Signaling Pathway. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    45019   Negative Regulation of Nitric Oxide Biosynthetic Process  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of the Chemical Reactions and Pathways Resulting in the Formation of Nitric Oxide. 
    45766   Positive Regulation of Angiogenesis  Any Process That Activates or Increases Angiogenesis. 
    50728   Negative Regulation of Inflammatory Response  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of the Inflammatory Response. 
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    71347   Cellular Response to Interleukin 1  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Interleukin 1 Stimulus. 
    71354   Cellular Response to Interleukin 6  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Interleukin 6 Stimulus. 
    71456   Cellular Response to Hypoxia  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus Indicating Lowered Oxygen Tension. Hypoxia Defined As a Decline in O2 Levels Below Normoxic Levels of 20.8 20.95% Results in Metabolic Adaptation At Both the Cellular and Organismal Level. 
    97190   Apoptotic Signaling Pathway  A Series of Molecular Signals Which Triggers the Apoptotic Death of a Cell. the Pathway Starts with Reception of a Signal and Ends When the Execution Phase of Apoptosis Is Triggered. 
    1900119   Positive Regulation of Execution Phase of Apoptosis  Any Process That Activates or Increases the Frequency Rate or Extent of Execution Phase of Apoptosis. 
    5615   Extracellular Space  That Part of a Multicellular Organism Outside the Cells Proper Usually Taken to Be Outside the Plasma Membranes and Occupied by Fluid. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    5783   Endoplasmic Reticulum  The Irregular Network of Unit Membranes Visible Only by Electron Microscopy That Occurs in the Cytoplasm of Many Eukaryotic Cells. the Membranes Form a Complex Meshwork of Tubular Channels Which Are Often Expanded Into Slitlike Cavities Called Cisternae. the Er Takes Two Forms Rough (or Granular) with Ribosomes Adhering to the Outer Surface and Smooth (with No Ribosomes Attached). 
    5789   Endoplasmic Reticulum Membrane  The Lipid Bilayer Surrounding the Endoplasmic Reticulum. 
    5901   Caveola  A Membrane Raft That Forms Small Pit Depression or Invagination That Communicates with the Outside of a Cell and Extends Inward Indenting the Cytoplasm and the Cell Membrane. Examples Include Any of the Minute Pits or Incuppings of the Cell Membrane Formed During Pinocytosis. Such Caveolae May Be Pinched Off to Form Free Vesicles Within the Cytoplasm. 
    16020   Membrane  A Lipid Bilayer Along with All the Proteins and Protein Complexes Embedded in It an Attached to It. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    4497   Monooxygenase Activity  Catalysis of the Incorporation of One Atom From Molecular Oxygen Into a Compound and the Reduction of the Other Atom of Oxygen to Water. 
    5506   Iron Ion Binding  Interacting Selectively and Non Covalently with Iron (fe) Ions. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    8116   Prostaglandin I Synthase Activity  Catalysis of the Reaction: Prostaglandin H(2) = Prostaglandin I(2). 
    16705   Oxidoreductase Activity Acting On Paired Donors with Incorporation or Reduction of Molecular Oxygen  Catalysis of an Oxidation Reduction (redox) Reaction in Which Hydrogen or Electrons Are Transferred From Each of Two Donors and Molecular Oxygen Is Reduced or Incorporated Into a Donor. 
    16853   Isomerase Activity  Catalysis of the Geometric or Structural Changes Within One Molecule. Isomerase Is the Systematic Name For Any Enzyme of EC Class 5. 
    20037   Heme Binding  Interacting Selectively and Non Covalently with Heme Any Compound of Iron Complexed in a Porphyrin (tetrapyrrole) Ring. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene ptgis
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Strain Bl21(de3) B834(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pCW
    Description Plasmid Pcw Was a Gift From Dr. Amy Roth University of Oregon.


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    20 20q13.13 5740     prostaglandin I2 (prostacyclin) synthase PTGIS    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs142630745 LS-SNP   dbSNP   A 26 R - > Q Coil 48% (Exposed) 20 48166724
    rs148875055 LS-SNP   dbSNP   A 53 F - > L Helix 2% (Buried) 20 48166644
    rs201673445 LS-SNP   dbSNP   A 62 G - > S Coil 38% (Exposed) 20 48166617
    rs11699426 LS-SNP   dbSNP   A 69 V - > G Beta Ladder 17% (Intermediate) 20 48164549
    rs182204601 LS-SNP   dbSNP   A 84 D - > N Helix 27% (Intermediate) 20 48164505
    rs139949009 LS-SNP   dbSNP   A 85 A - > T Helix 25% (Intermediate) 20 48164502
    rs77466832 LS-SNP   dbSNP   A 86 V - > G Helix 1% (Buried) 20 48164498
    rs200631702 LS-SNP   dbSNP   A 91 R - > C Turn 44% (Exposed) 20 48164484
    rs144185728 LS-SNP   dbSNP   A 91 R - > H Turn 44% (Exposed) 20 48164483
    rs199740067 LS-SNP   dbSNP   A 95 D - > N Beta Ladder 12% (Intermediate) 20 48164472
    rs148315757 LS-SNP   dbSNP   A 109 D - > Y Coil 28% (Intermediate) 20 48164430
    rs5622 LS-SNP   dbSNP   A 118 S - > R Helix 55% (Exposed) 20 48164401
    rs6067121 LS-SNP   dbSNP   A 134 Q - > H Helix 42% (Exposed) 20 48160961
    rs13306023 LS-SNP   dbSNP   A 140 M - > T Helix 0% (Buried) 20 48160944
    rs201485016 LS-SNP   dbSNP   A 151 D - > N Helix 23% (Intermediate) 20 48160912
    rs5623 LS-SNP   dbSNP   A 154 E - > A Helix 71% (Exposed) 20 48160902
    rs199526901 LS-SNP   dbSNP   A 166 D - > N Helix 38% (Exposed) 20 48160867
    rs5624 LS-SNP   dbSNP   A 171 F - > L Helix 1% (Buried) 20 48160852
    rs200101009 LS-SNP   dbSNP   A 176 G - > D Helix 0% (Buried) 20 48156253
    rs148768155 LS-SNP   dbSNP   A 182 G - > R Coil 0% (Buried) 20 48156236
    rs145481145 LS-SNP   dbSNP   A 188 R - > C Coil 25% (Intermediate) 20 48156218
    rs139965033 LS-SNP   dbSNP   A 197 R - > C Helix 14% (Intermediate) 20 48156191
    rs200223463 LS-SNP   dbSNP   A 198 V - > I Helix 61% (Exposed) 20 48156188
    rs145802460 LS-SNP   dbSNP   A 208 R - > H Helix 4% (Buried) 20 48156157
    rs143394422 LS-SNP   dbSNP   A 211 D - > N Helix 0% (Buried) 20 48156149
    rs201920776 LS-SNP   dbSNP   A 212 R - > W Helix 47% (Exposed) 20 48156146
    rs138058562 LS-SNP   dbSNP   A 219 R - > C Helix 43% (Exposed) 20 48156125
    rs201288052 LS-SNP   dbSNP   A 225 G - > E Helix 55% (Exposed) 20 48140776
    rs13306030 LS-SNP   dbSNP   A 227 K - > T Helix 50% (Exposed) 20 48140770
    rs150320603 LS-SNP   dbSNP   A 229 H - > D Helix 39% (Exposed) 20 48140765
    rs5626 LS-SNP   dbSNP   A 236 R - > C Helix 42% (Exposed) 20 48140744
    rs151196959 LS-SNP   dbSNP   A 240 L - > Q Helix 2% (Buried) 20 48140731
    rs141132754 LS-SNP   dbSNP   A 242 S - > F Coil 18% (Intermediate) 20 48140725
    rs146513003 LS-SNP   dbSNP   A 249 R - > W Coil 7% (Buried) 20 48140705
    rs45571835 LS-SNP   dbSNP   A 249 R - > LQ Coil 7% (Buried) 20 48140704
    rs145783271 LS-SNP   dbSNP   A 252 R - > W Coil 21% (Intermediate) 20 48140696
    rs200499141 LS-SNP   dbSNP   A 261 L - > Q Helix 59% (Exposed) 20 48140668
    rs201480227 LS-SNP   dbSNP   A 272 M - > T Helix 19% (Intermediate) 20 48140635
    rs61734270 LS-SNP   dbSNP   A 275 R - > Q Helix 29% (Intermediate) 20 48140626
    rs150671072 LS-SNP   dbSNP   A 275 R - > W Helix 29% (Intermediate) 20 48140627
    rs151193790 LS-SNP   dbSNP   A 278 V - > M Helix 0% (Buried) 20 48140618
    rs140218468 LS-SNP   dbSNP   A 288 M - > V Helix 4% (Buried) 20 48130926 HEM
    rs150077993 LS-SNP   dbSNP   A 310 R - > HL Helix 10% (Intermediate) 20 48130859
    rs199876310 LS-SNP   dbSNP   A 344 V - > M Helix 0% (Buried) 20 48129793
    rs201137032 LS-SNP   dbSNP   A 350 R - > S Helix 0% (Buried) 20 48129773
    rs147983323 LS-SNP   dbSNP   A 359 R - > H Beta Ladder 2% (Buried) 20 48129747
    rs149277612 LS-SNP   dbSNP   A 376 N - > S Beta Ladder 36% (Intermediate) 20 48129696
    rs56195291 LS-SNP   dbSNP   A 379 R - > GS Turn 68% (Exposed) 20 48129688
    rs144816768 LS-SNP   dbSNP   A 426 R - > Q Beta Ladder 54% (Exposed) 20 48127646
    rs140986161 LS-SNP   dbSNP   A 432 M - > I Coil 4% (Buried) 20 48127627
    rs146531327 LS-SNP   dbSNP   A 447 A - > T Helix 12% (Intermediate) 20 48127584 HEM
    rs145551841 LS-SNP   dbSNP   A 460 V - > M Helix 15% (Intermediate) 20 48124582
    rs199725387 LS-SNP   dbSNP   A 469 A - > T Turn 64% (Exposed) 20 48124555
    rs201918056 LS-SNP   dbSNP   A 469 A - > V Turn 64% (Exposed) 20 48124554
    rs140373444 LS-SNP   dbSNP   A 482 G - > S Beta 19% (Intermediate) 20 48124516
    rs151253565 LS-SNP   dbSNP   A 488 P - > L Beta 10% (Intermediate) 20 48124497
    rs201583708 LS-SNP   dbSNP   A 491 D - > E Coil 27% (Intermediate) 20 48124487
    rs200895888 LS-SNP   dbSNP   A 492 V - > L Coil 1% (Buried) 20 48124486
    rs142254215 LS-SNP   dbSNP   A 494 V - > I Beta Ladder 0% (Buried) 20 48124480
    rs149173992 LS-SNP   dbSNP   A 495 R - > H Beta Ladder 12% (Intermediate) 20 48124476
    rs5584 LS-SNP   dbSNP   A 500 P - > S Coil 47% (Exposed) 20 48124462