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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN LEUKOTRIENE C4 SYNTHASE
 
Authors :  D. Martinez Molina, A. Wetterholm, A. Kohl, A. A. Mccarthy, D. Niegowski, E. Ohlson, T. Hammarberg, S. Eshaghi, J. Z. Haeggstrom, P. Nordlund
Date :  02 Mar 07  (Deposition) - 17 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Leukotriene Signalling, Leukotriene Biosynthesis, Membrane, Eicosanoid, Transmembrane, Membrane Protein, Apo, Lyase, Mapeg, Human, Ltc4S, Enzyme, Trimer (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Martinez Molina, A. Wetterholm, A. Kohl, A. A. Mccarthy, D. Niegowski, E. Ohlson, T. Hammarberg, S. Eshaghi, J. Z. Haeggstrom, P. Nordlund
Structural Basis For Synthesis Of Inflammatory Mediators By Human Leukotriene C4 Synthase.
Nature V. 448 613 2007
PubMed-ID: 17632546  |  Reference-DOI: 10.1038/NATURE06009

(-) Compounds

Molecule 1 - LEUKOTRIENE C4 SYNTHASE
    ChainsA
    EC Number4.4.1.20
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPICZ
    Expression System StrainKM71H
    Expression System Taxid4922
    FragmentRESIDUES 2-150
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLEUKOTRIENE-C(4) SYNTHASE, LTC4 SYNTHASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1LMT2Ligand/IonDODECYL-BETA-D-MALTOSIDE
2NI3Ligand/IonNICKEL (II) ION
3PLM14Ligand/IonPALMITIC ACID
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 54)
No.NameCountTypeFull Name
1LMT6Ligand/IonDODECYL-BETA-D-MALTOSIDE
2NI-1Ligand/IonNICKEL (II) ION
3PLM42Ligand/IonPALMITIC ACID
4SO46Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:-1 , HIS A:1BINDING SITE FOR RESIDUE NI A1151
02AC2SOFTWAREHIS A:-4 , HIS A:-2BINDING SITE FOR RESIDUE NI A1152
03AC3SOFTWAREHIS A:-2 , HOH A:2001BINDING SITE FOR RESIDUE NI A1153
04AC4SOFTWARETYR A:109 , ARG A:113 , TRP A:116 , LMT A:1155BINDING SITE FOR RESIDUE LMT A1154
05AC5SOFTWAREILE A:27 , ARG A:31 , ARG A:104 , LEU A:108 , TYR A:109 , TRP A:116 , LMT A:1154 , PLM A:1160 , SO4 A:1165 , HOH A:2101 , HOH A:2102 , HOH A:2105BINDING SITE FOR RESIDUE LMT A1155
06AC6SOFTWAREPRO A:132 , LEU A:135BINDING SITE FOR RESIDUE PLM A1170
07AC7SOFTWARELEU A:84BINDING SITE FOR RESIDUE PLM A1171
08AC8SOFTWARELEU A:14 , GLY A:77 , LEU A:81 , LEU A:84BINDING SITE FOR RESIDUE PLM A1173
09AC9SOFTWARELEU A:18 , GLN A:95 , HOH A:2016BINDING SITE FOR RESIDUE PLM A1156
10BC1SOFTWARELEU A:7 , PHE A:130 , PLM A:1159 , PLM A:1161 , HOH A:2087BINDING SITE FOR RESIDUE PLM A1157
11BC2SOFTWARELEU A:14 , PHE A:88BINDING SITE FOR RESIDUE PLM A1158
12BC3SOFTWARELEU A:13 , PHE A:130 , PLM A:1157BINDING SITE FOR RESIDUE PLM A1159
13BC4SOFTWAREARG A:99 , GLN A:102BINDING SITE FOR RESIDUE PLM A1175
14BC5SOFTWARELMT A:1155BINDING SITE FOR RESIDUE PLM A1160
15BC6SOFTWAREHIS A:75 , GLU A:76 , GLY A:77 , ARG A:144 , PLM A:1157 , PLM A:1162 , PLM A:1163 , HOH A:2062 , HOH A:2064BINDING SITE FOR RESIDUE PLM A1161
16BC7SOFTWAREGLU A:4 , GLY A:71 , ILE A:72 , PLM A:1161 , PLM A:1163 , HOH A:2008 , HOH A:2106BINDING SITE FOR RESIDUE PLM A1162
17BC8SOFTWAREHIS A:0 , LYS A:2 , HIS A:75 , ARG A:136 , PLM A:1161 , PLM A:1162BINDING SITE FOR RESIDUE PLM A1163
18BC9SOFTWARESER A:100 , ALA A:101 , GLN A:102 , HOH A:2108BINDING SITE FOR RESIDUE SO4 A1164
19CC1SOFTWAREASN A:55 , TYR A:93 , ARG A:104 , LEU A:108 , LMT A:1155 , HOH A:2102 , HOH A:2109 , HOH A:2110BINDING SITE FOR RESIDUE SO4 A1165

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2UUI)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1His A:-4 -His A:-3
2Pro A:37 -Pro A:38
3Arg A:144 -Thr A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042736R142QLTC4S_HUMANPolymorphism11541078AR142Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042736R142QLTC4S_HUMANPolymorphism11541078AR142Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FLAP_GST2_LTC4SPS01297 FLAP/GST2/LTC4S family signature.LTC4S_HUMAN42-56  1A:42-56
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FLAP_GST2_LTC4SPS01297 FLAP/GST2/LTC4S family signature.LTC4S_HUMAN42-56  3A:42-56

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002925961cENSE00001194180chr5:179220987-179221139153LTC4S_HUMAN1-20201A:1-2020
1.3bENST000002925963bENSE00001056000chr5:179222585-179222684100LTC4S_HUMAN20-53341A:20-5334
1.3fENST000002925963fENSE00001255861chr5:179222787-17922285771LTC4S_HUMAN53-77251A:53-7725
1.3gENST000002925963gENSE00001056001chr5:179222942-17922302382LTC4S_HUMAN77-104281A:77-10428
1.4eENST000002925964eENSE00002050377chr5:179223254-179223513260LTC4S_HUMAN104-150471A:104-15047

(-) 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:156
 aligned with LTC4S_HUMAN | Q16873 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:156
                                  1                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144      
          LTC4S_HUMAN     - ------MKDEVALLAAVTLLGVLLQAYFSLQVISARRAFRVSPPLTTGPPEFERVYRAQVNCSEYFPLFLATLWVAGIFFHEGAAALCGLVYLFARLRYFQGYARSAQLRLAPLYASARALWLLVALAALGLLAHFLPAALRAALLGRLRTLLPWA 150
               SCOP domains -------d2uuia1 A:2-147 Leukotriene C4 synthase                                                                                                           --- SCOP domains
               CATH domains 2uuiA00 A:-5-150 MAPEG domain-like                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------Q-------- SAPs(SNPs)
                    PROSITE -----------------------------------------------FLAP_GST2_LTC4S---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ------Exon 1.1c           --------------------------------Exon 1.3f  PDB: A:53-77  --------------------------Exon 1.4e  PDB: A:104-150 UniProt: 104-150      Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.3b  PDB: A:20-53           -----------------------Exon 1.3g  PDB: A:77-104    ---------------------------------------------- Transcript 1 (2)
                 2uui A  -5 MHHHHHHKDEVALLAAVTLLGVLLQAYFSLQVISARRAFRVSPPLTTGPPEFERVYRAQVNCSEYFPLFLATLWVAGIFFHEGAAALCGLVYLFARLRYFQGYARSAQLRLAPLYASARALWLLVALAALGLLAHFLPAALRAALLGRLRTLLPWA 150
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144      

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2UUI)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A   (LTC4S_HUMAN | Q16873)
molecular function
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    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:0004602    glutathione peroxidase activity    Catalysis of the reaction: 2 glutathione + hydrogen peroxide = oxidized glutathione + 2 H2O.
    GO:0004364    glutathione transferase activity    Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
    GO:0004464    leukotriene-C4 synthase activity    Catalysis of the reaction: leukotriene C(4) = glutathione + leukotriene A(4).
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0005515    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).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0071222    cellular response to lipopolysaccharide    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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0071299    cellular response to vitamin A    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 vitamin A stimulus.
    GO:0019370    leukotriene biosynthetic process    The chemical reactions and pathways resulting in the formation of leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid.
    GO:0006691    leukotriene metabolic process    The chemical reactions and pathways involving leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid.
    GO:2001300    lipoxin metabolic process    The chemical reactions and pathways involving a lipoxin. A lipoxin is a non-classic eicosanoid and signalling molecule that has four conjugated double bonds and is derived from arachidonic acid.
    GO:0019372    lipoxygenase pathway    The chemical reactions and pathways by which an unsaturated fatty acid (such as arachidonic acid or linolenic acid) is converted to other compounds, and in which the first step is hydroperoxide formation catalyzed by lipoxygenase.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0048678    response to axon injury    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 axon injury stimulus.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0010035    response to inorganic substance    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 inorganic substance 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.
cellular component
    GO:0005783    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).
    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:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005640    nuclear outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
    GO:0005634    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LTC4S_HUMAN | Q168732pno 2uuh 3b29 3hkk 3leo 3pcv 4bpm 4j7t 4j7y 4jc7 4jcz 4jrz 4wab 5hv9

(-) Related Entries Specified in the PDB File

2uuh CRYSTAL STRUCTURE OF HUMAN LEOKOTRIENE C4 SYNTHASE WITH SUBSTRATE GLUTATHIONE BOUND