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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

Molecule 1 - LEUKOTRIENE C4 SYNTHASE
	Chains	:	A
	EC Number	:	4.4.1.20
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZ
	Expression System Strain	:	KM71H
	Expression System Taxid	:	4922
	Fragment	:	RESIDUES 2-150
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LEUKOTRIENE-C(4) SYNTHASE, LTC4 SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 21)

No.	Name	Count	Type	Full Name
1	LMT	2	Ligand/Ion	DODECYL-BETA-D-MALTOSIDE
2	NI	3	Ligand/Ion	NICKEL (II) ION
3	PLM	14	Ligand/Ion	PALMITIC ACID
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 54)

No.	Name	Count	Type	Full Name
1	LMT	6	Ligand/Ion	DODECYL-BETA-D-MALTOSIDE
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PLM	42	Ligand/Ion	PALMITIC ACID
4	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:-1 , HIS A:1	BINDING SITE FOR RESIDUE NI A1151
02	AC2	SOFTWARE	HIS A:-4 , HIS A:-2	BINDING SITE FOR RESIDUE NI A1152
03	AC3	SOFTWARE	HIS A:-2 , HOH A:2001	BINDING SITE FOR RESIDUE NI A1153
04	AC4	SOFTWARE	TYR A:109 , ARG A:113 , TRP A:116 , LMT A:1155	BINDING SITE FOR RESIDUE LMT A1154
05	AC5	SOFTWARE	ILE 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:2105	BINDING SITE FOR RESIDUE LMT A1155
06	AC6	SOFTWARE	PRO A:132 , LEU A:135	BINDING SITE FOR RESIDUE PLM A1170
07	AC7	SOFTWARE	LEU A:84	BINDING SITE FOR RESIDUE PLM A1171
08	AC8	SOFTWARE	LEU A:14 , GLY A:77 , LEU A:81 , LEU A:84	BINDING SITE FOR RESIDUE PLM A1173
09	AC9	SOFTWARE	LEU A:18 , GLN A:95 , HOH A:2016	BINDING SITE FOR RESIDUE PLM A1156
10	BC1	SOFTWARE	LEU A:7 , PHE A:130 , PLM A:1159 , PLM A:1161 , HOH A:2087	BINDING SITE FOR RESIDUE PLM A1157
11	BC2	SOFTWARE	LEU A:14 , PHE A:88	BINDING SITE FOR RESIDUE PLM A1158
12	BC3	SOFTWARE	LEU A:13 , PHE A:130 , PLM A:1157	BINDING SITE FOR RESIDUE PLM A1159
13	BC4	SOFTWARE	ARG A:99 , GLN A:102	BINDING SITE FOR RESIDUE PLM A1175
14	BC5	SOFTWARE	LMT A:1155	BINDING SITE FOR RESIDUE PLM A1160
15	BC6	SOFTWARE	HIS 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:2064	BINDING SITE FOR RESIDUE PLM A1161
16	BC7	SOFTWARE	GLU A:4 , GLY A:71 , ILE A:72 , PLM A:1161 , PLM A:1163 , HOH A:2008 , HOH A:2106	BINDING SITE FOR RESIDUE PLM A1162
17	BC8	SOFTWARE	HIS A:0 , LYS A:2 , HIS A:75 , ARG A:136 , PLM A:1161 , PLM A:1162	BINDING SITE FOR RESIDUE PLM A1163
18	BC9	SOFTWARE	SER A:100 , ALA A:101 , GLN A:102 , HOH A:2108	BINDING SITE FOR RESIDUE SO4 A1164
19	CC1	SOFTWARE	ASN A:55 , TYR A:93 , ARG A:104 , LEU A:108 , LMT A:1155 , HOH A:2102 , HOH A:2109 , HOH A:2110	BINDING SITE FOR RESIDUE SO4 A1165

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

Asymmetric Unit

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

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_042736	R	142	Q	LTC4S_HUMAN	Polymorphism	11541078	A	R	142	Q

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

Biological Unit 1 (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_042736	R	142	Q	LTC4S_HUMAN	Polymorphism	11541078	A	R	142	Q

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAP_GST2_LTC4S	PS01297	FLAP/GST2/LTC4S family signature.	LTC4S_HUMAN	42-56	1	A:42-56

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAP_GST2_LTC4S	PS01297	FLAP/GST2/LTC4S family signature.	LTC4S_HUMAN	42-56	3	A:42-56

Asymmetric Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000292596	1c	ENSE00001194180	chr5:179220987-179221139	153	LTC4S_HUMAN	1-20	20	1	A:1-20	20
1.3b	ENST00000292596	3b	ENSE00001056000	chr5:179222585-179222684	100	LTC4S_HUMAN	20-53	34	1	A:20-53	34
1.3f	ENST00000292596	3f	ENSE00001255861	chr5:179222787-179222857	71	LTC4S_HUMAN	53-77	25	1	A:53-77	25
1.3g	ENST00000292596	3g	ENSE00001056001	chr5:179222942-179223023	82	LTC4S_HUMAN	77-104	28	1	A:77-104	28
1.4e	ENST00000292596	4e	ENSE00002050377	chr5:179223254-179223513	260	LTC4S_HUMAN	104-150	47	1	A:104-150	47

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)
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	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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Membrane and cell surface proteins and peptides (2046)

Fold: MAPEG domain-like (9)

Superfamily: MAPEG domain-like (9)

Family: MAPEG domain (7)

Protein domain: Leukotriene C4 synthase (4)

Human (Homo sapiens) [TaxId: 9606] (4)

d2uuia1

A:2-147

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: MAPEG domain-like (7)

Human (Homo sapiens) (6)

2uuiA00

A:-5-150

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

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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	Cis Peptide Bonds
		Arg A:144 - Thr A:145	[ RasMol ]
		His A:-4 - His A:-3	[ RasMol ]
		Pro A:37 - Pro A:38	[ RasMol ]

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	LTC4S_HUMAN \| Q16873	:	2pno 2uuh 3b29 3hkk 3leo 3pcv 4bpm 4j7t 4j7y 4jc7 4jcz 4jrz 4wab 5hv9

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 21)

Sites (19, 19)

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