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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN INTEGRAL MEMBRANE ENZYME
 
Authors :  D. Li, M. Wang, V. Olieric, M. Caffrey
Date :  27 May 13  (Deposition) - 16 Apr 14  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Isomerase, Cancer, Drug Target, In Meso Crystallization, Inflammation, Inhibitor, Leukotriene C4 Synthase, Lipid Metabolism, Membrane-Associated Proteins In Eicosanoid And Glutathione Metabolism, Mapag, Membrane Protein, Mpges1, Pain, Microcrystal, Anomalous Dispersion, Sulfur-Sad, S-Sad (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Li, N. Howe, A. Dukkipati, S. T. A. Shah, B. D. Bax, C. Edge, A. Bridges P. Hardwicke, O. M. P. Singh, G. Giblin, A. Pautsch, R. Pfau, G. Schnapp M. Wang, V. Olieric, M. Caffrey
Crystallizing Membrane Proteins In The Lipidic Mesophase. Experience With Human Prostaglandin E2 Synthase 1 And An Evolving Strategy.
Cryst. Growth Des. V. 14 2034 2014
PubMed-ID: 24803849  |  Reference-DOI: 10.1021/CG500157X

(-) Compounds

Molecule 1 - PROSTAGLANDIN E SYNTHASE, FUSION PEPTIDE
    ChainsA
    EC Number5.3.99.3
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFB1-6H-MPGES (10-152)-F-LTC4S
    Expression System Taxid7108
    Expression System VectorPFASTBAC1
    FragmentGSH-BINDING MOTIF, RESIDUES 10-152
    MutationYES
    Organism ScientificHOMO SAPIENS, SYNTHETIC CONSTRUCT
    Organism Taxid9606, 32630
    SynonymMICROSOMAL GLUTATHIONE S-TRANSFERASE 1-LIKE 1, MGST1-L1, MICROSOMAL PROSTAGLANDIN E SYNTHASE 1, MPGES-1, P53-INDUCED GENE 12 PROTEIN, PROSTAGLANDIN E2 SYNTHASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GSH1Ligand/IonGLUTATHIONE
2LVJ1Ligand/Ion2-[[2,6-BIS(CHLORANYL)-3-[(2,2-DIMETHYLPROPANOYLAMINO)METHYL]PHENYL]AMINO]-1-METHYL-6-(2-METHYL-2-OXIDANYL-PROPOXY)-N-[2,2,2-TRIS(FLUORANYL)ETHYL]BENZIMIDAZOLE-5-CARBOXAMIDE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GSH3Ligand/IonGLUTATHIONE
2LVJ3Ligand/Ion2-[[2,6-BIS(CHLORANYL)-3-[(2,2-DIMETHYLPROPANOYLAMINO)METHYL]PHENYL]AMINO]-1-METHYL-6-(2-METHYL-2-OXIDANYL-PROPOXY)-N-[2,2,2-TRIS(FLUORANYL)ETHYL]BENZIMIDAZOLE-5-CARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:31 , THR A:34 , ARG A:38 , LEU A:69 , ARG A:70 , ARG A:73 , ASN A:74 , GLU A:77 , HIS A:113 , TYR A:117 , ARG A:126 , SER A:127 , TYR A:130 , LVJ A:1173 , HOH A:2004 , HOH A:2024 , HOH A:2037BINDING SITE FOR RESIDUE GSH A 1172
2AC2SOFTWAREGLY A:35 , GLN A:36 , LEU A:39 , ASP A:49 , ARG A:52 , HIS A:53 , ALA A:123 , PRO A:124 , SER A:127 , VAL A:128 , THR A:131 , LEU A:132 , GSH A:1172BINDING SITE FOR RESIDUE LVJ A 1173

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BPM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BPM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BPM)

(-) Exons   (0, 0)

(no "Exon" information available for 4BPM)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:162
 aligned with PTGES_HUMAN | O14684 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:162
                                                                                                                                                                        152                   
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149  |      -         -  
          PTGES_HUMAN    10 SPALPAFLLCSTLLVIKMYVVAIITGQVRLRKKAFANPEDALRHGGPQYCRSDPDVERCLRAHRNDMETIYPFLFLGFVYSFLGPNPFVAWMHFLVFLVGRVAHTVAYLGKLRAPIRSVTYTLAQLPCASMALQILWEAARHL-------------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bpm A  10 SPALPAFLLCSTLLVIKMYVVAIITGQVRLRKKAFANPEDALRHGGPQYCRSDPDVERCLRAHRNDMETIYPFLFLGFVYSFLGPNPFVAWMHFLVFLVGRVAHTVAYLGKLRAPIRSVTYTLAQLPCASMALQILWEAARHFLPAALRAALLGRLRTLRPW 171
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4BPM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BPM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BPM)

(-) Gene Ontology  (48, 54)

Asymmetric Unit(hide GO term definitions)
Chain A   (PTGES_HUMAN | O14684)
molecular function
    GO:0043295    glutathione binding    Interacting selectively and non-covalently with glutathione; a tripeptide composed of the three amino acids cysteine, glutamic acid and glycine.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0050220    prostaglandin-E synthase activity    Catalysis of the reaction: prostaglandin H(2) = prostaglandin E(2).
biological process
    GO:0002526    acute inflammatory response    Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
    GO:0002544    chronic inflammatory response    Inflammation of prolonged duration (weeks or months) in which active inflammation, tissue destruction, and attempts at repair are proceeding simultaneously. Although it may follow acute inflammation, chronic inflammation frequently begins insidiously, as a low-grade, smoldering, often asymptomatic response.
    GO:0019371    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.
    GO:0006633    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.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    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.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0001516    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.
    GO:0006693    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.
    GO:0051592    response to calcium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
    GO:0034097    response to cytokine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0032526    response to retinoic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005641    nuclear envelope lumen    The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LTC4S_HUMAN | Q168732pno 2uuh 2uui 3b29 3hkk 3leo 3pcv 4j7t 4j7y 4jc7 4jcz 4jrz 4wab 5hv9
        PTGES_HUMAN | O146843dww 4al0 4al1 4wab 4yk5 4yl0 4yl1 4yl3 5bqg 5bqh 5bqi 5k0i 5t36 5t37 5tl9

(-) Related Entries Specified in the PDB File

4bpd CRYSTAL STRUCTURE OF AN INTEGRAL MEMBRANE ENZYME DGKA- V1