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Asym./Biol. Unit (Jmol Viewer)

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Title :   HUMAN GLUTATHIONE S-TRANSFERASE M2-2 (E.C.2.5.1.18) COMPLEXED WITH GLUTATHIONE-DISULFIDE

Authors :   Y. V. Patskovsky, L. N. Patskovska, I. Listowsky, S. C. Almo

Date :   17 Jan 05 (Deposition) - 25 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Transferase, Glutathione, Conjugation, Glutathione-Disulfide, Prostaglandin E2, Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. V. Patskovsky, L. N. Patskovska, I. Listowsky, S. C. Almo
Selective Inhibitors Of Prostaglandin Synthase Activity Of Human Glutathione S-Transferase M2-2
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GLUTATHIONE S-TRANSFERASE MU 2
	Chains	:	A, B
	EC Number	:	2.5.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A-HGSTM2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET3A
	Gene	:	GSTM2, GST4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GSTM2-2, GST CLASS-MU 2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GDS	2	Ligand/Ion	OXIDIZED GLUTATHIONE DISULFIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:6 , TRP A:7 , GLY A:11 , LEU A:12 , ARG A:42 , TRP A:45 , LYS A:49 , ASN A:58 , LEU A:59 , GLN A:71 , SER A:72 , ARG A:107 , ALA A:111 , TYR A:115 , ARG A:165 , PHE A:208 , HOH A:404 , HOH A:421 , HOH A:467 , HOH A:469 , HOH A:589 , ASP B:105	BINDING SITE FOR RESIDUE GDS A 400
2	AC2	SOFTWARE	ASP A:105 , HOH A:484 , TYR B:6 , TRP B:7 , GLY B:11 , LEU B:12 , ARG B:42 , TRP B:45 , LYS B:49 , ASN B:58 , LEU B:59 , GLN B:71 , SER B:72 , ARG B:107 , ALA B:111 , TYR B:115 , ARG B:165 , PHE B:208 , HOH B:415 , HOH B:492 , HOH B:505 , HOH B:538 , HOH B:548 , HOH B:585 , HOH B:589 , HOH B:599	BINDING SITE FOR RESIDUE GDS B 401

(no "SS Bond" information available for 1YKC)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:37	-	Pro A:38
2	Leu A:59	-	Pro A:60
3	Arg A:205	-	Pro A:206
4	Ala B:37	-	Pro B:38
5	Leu B:59	-	Pro B:60
6	Arg B:205	-	Pro B:206

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049486	S	173	N	GSTM2_HUMAN	Polymorphism	2229050	A/B	S	172	N

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GST_CTER	PS50405	Soluble glutathione S-transferase C-terminal domain profile.	GSTM2_HUMAN	90-208	2	A:89-207 B:89-207

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1j	ENST00000241337	1j	ENSE00001898781	chr1:110210724-110210773	50	GSTM2_HUMAN	1-12	12	2	A:1-11 B:1-11	11 11
1.2b	ENST00000241337	2b	ENSE00001732758	chr1:110211047-110211122	76	GSTM2_HUMAN	13-38	26	2	A:12-37 B:12-37	26 26
1.2d	ENST00000241337	2d	ENSE00001662058	chr1:110211547-110211611	65	GSTM2_HUMAN	38-59	22	2	A:37-58 B:37-58	22 22
1.3b	ENST00000241337	3b	ENSE00001605407	chr1:110211912-110211993	82	GSTM2_HUMAN	60-87	28	2	A:59-86 B:59-86	28 28
1.4a	ENST00000241337	4a	ENSE00001630516	chr1:110212093-110212193	101	GSTM2_HUMAN	87-120	34	2	A:86-119 B:86-119	34 34
1.6b	ENST00000241337	6b	ENSE00001681310	chr1:110213909-110214004	96	GSTM2_HUMAN	121-152	32	2	A:120-151 B:120-151	32 32
1.7b	ENST00000241337	7b	ENSE00001746057	chr1:110214095-110214205	111	GSTM2_HUMAN	153-189	37	2	A:152-188 B:152-188	37 37
1.9e	ENST00000241337	9e	ENSE00001826241	chr1:110217369-110217908	540	GSTM2_HUMAN	190-218	29	2	A:189-217 B:189-217	29 29

Asymmetric/Biological 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:217
 aligned with GSTM2_HUMAN | P28161 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
          GSTM2_HUMAN     2 PMTLGYWNIRGLAHSIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGTHKITQSNAILRYIARKHNLCGESEKEQIREDILENQFMDSRMQLAKLCYDPDFEKLKPEYLQALPEMLKLYSQFLGKQPWFLGDKITFVDFIAYDVLERNQVFEPSCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFTKMAVWGNK 218
               SCOP domains d1ykca2 A:1-84 Class mu GST                                                         d1ykca1 A:85-217 Class mu GST                                                                                                         SCOP domains
               CATH domains 1ykcA01 A:1-85,A:191-217 Glutaredoxin                                                1ykcA02 A:86-190  [code=1.20.1050.10, no name defined]                                                   1ykcA01 A:1-85,A:191-217    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...eeeeee.........hhhhhhhhhhh........eeee..eeeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------N--------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------GST_CTER  PDB: A:89-207 UniProt: 90-208                                                                                ---------- PROSITE
           Transcript 1 (1) Exon 1.1j  Exon 1.2b  PDB: A:12-37   ---------------------Exon 1.3b  PDB: A:59-86     ---------------------------------Exon 1.6b  PDB: A:120-151       Exon 1.7b  PDB: A:152-188            Exon 1.9e  PDB: A:189-217     Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.2d  PDB: A:37-5---------------------------Exon 1.4a  PDB: A:86-119          -------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1ykc A   1 PMTLGYWNIRGLAHSIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGTHKITQSNAILRYIARKHNLCGESEKEQIREDILENQFMDSRMQLAKLCYDPDFEKLKPEYLQALPEMLKLYSQFLGKQPWFLGDKITFVDFIAYDVLERNQVFEPSCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFTKMAVWGNK 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with GSTM2_HUMAN | P28161 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
          GSTM2_HUMAN     2 PMTLGYWNIRGLAHSIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGTHKITQSNAILRYIARKHNLCGESEKEQIREDILENQFMDSRMQLAKLCYDPDFEKLKPEYLQALPEMLKLYSQFLGKQPWFLGDKITFVDFIAYDVLERNQVFEPSCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFTKMAVWGNK 218
               SCOP domains d1ykcb2 B:1-84 Class mu GST                                                         d1ykcb1 B:85-217 Class mu GST                                                                                                         SCOP domains
               CATH domains 1ykcB01 B:1-85,B:191-217 Glutaredoxin                                                1ykcB02 B:86-190  [code=1.20.1050.10, no name defined]                                                   1ykcB01 B:1-85,B:191-217    CATH domains
           Pfam domains (1) -GST_N-1ykcB03 B:2-81                                                            ---------------------GST_C-1ykcB01 B:103-191                                                                  -------------------------- Pfam domains (1)
           Pfam domains (2) -GST_N-1ykcB04 B:2-81                                                            ---------------------GST_C-1ykcB02 B:103-191                                                                  -------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...eeeeee.........hhhhhh.............eeee..eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------N--------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------GST_CTER  PDB: B:89-207 UniProt: 90-208                                                                                ---------- PROSITE
           Transcript 1 (1) Exon 1.1j  Exon 1.2b  PDB: B:12-37   ---------------------Exon 1.3b  PDB: B:59-86     ---------------------------------Exon 1.6b  PDB: B:120-151       Exon 1.7b  PDB: B:152-188            Exon 1.9e  PDB: B:189-217     Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.2d  PDB: B:37-5---------------------------Exon 1.4a  PDB: B:86-119          -------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1ykc B   1 PMTLGYWNIRGLAHSIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGTHKITQSNAILRYIARKHNLCGESEKEQIREDILENQFMDSRMQLAKLCYDPDFEKLKPEYLQALPEMLKLYSQFLGKQPWFLGDKITFVDFIAYDVLERNQVFEPSCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFTKMAVWGNK 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: GST C-terminal domain-like (353)

Superfamily: GST C-terminal domain-like (353)

Family: Glutathione S-transferase (GST), C-terminal domain (263)

Protein domain: Class mu GST (33)

Human (Homo sapiens) [TaxId: 9606] (15)

1a	d1ykca1	A:85-217
1b	d1ykcb1	B:85-217

Class: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Glutathione S-transferase (GST), N-terminal domain (216)

Protein domain: Class mu GST (33)

Human (Homo sapiens) [TaxId: 9606] (15)

2a	d1ykca2	A:1-84
2b	d1ykcb2	B:1-84

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Human (Homo sapiens) (186)

1a	1ykcA01	A:1-85,A:191-217
1b	1ykcB01	B:1-85,B:191-217

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 (267)

Homologous Superfamily: [code=1.20.1050.10, no name defined] (249)

Human (Homo sapiens) (119)

2a	1ykcA02	A:86-190
2b	1ykcB02	B:86-190

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GST_C (118)

Family: GST_C (102)

Homo sapiens (Human) (47)

1a	GST_C-1ykcB01	B:103-191
1b	GST_C-1ykcB02	B:103-191

Clan: Thioredoxin (367)

Family: GST_N (88)

Homo sapiens (Human) (45)

2a	GST_N-1ykcB03	B:2-81
2b	GST_N-1ykcB04	B:2-81

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GSTM2_HUMAN | P28161)

molecular function
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any 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: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: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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0070458	cellular detoxification of nitrogen compound	Any cellular process that reduces or removes the toxicity of nitrogenous compounds which are dangerous or toxic. This includes the aerobic conversion of toxic compounds to harmless substances.
	GO:0071313	cellular response to caffeine	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 caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
	GO:1901687	glutathione derivative biosynthetic process	The chemical reactions and pathways resulting in the formation of glutathione derivative.
	GO:0006749	glutathione metabolic process	The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0060315	negative regulation of ryanodine-sensitive calcium-release channel activity	Any process that decreases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
	GO:0018916	nitrobenzene metabolic process	The chemical reactions and pathways involving nitrobenzene (nitrobenzol), a derivative of benzene with an NO2 group attached to the ring. It is a yellow aromatic liquid used in perfumery and manufactured in large quantities in the preparation of aniline.
	GO:0060316	positive regulation of ryanodine-sensitive calcium-release channel activity	Any process that increases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
	GO:0010881	regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion	Any process that modulates the frequency, rate or extent of cardiac muscle contraction via the regulation of the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol. The sarcoplasmic reticulum is the endoplasmic reticulum of striated muscle, specialised for the sequestration of calcium ions that are released upon receipt of a signal relayed by the T tubules from the neuromuscular junction.
	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
	GO:0014809	regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion	Any process that modulates the frequency, rate or extent of skeletal muscle contraction via the regulation of the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol. The sarcoplasmic reticulum is the endoplasmic reticulum of striated muscle, specialised for the sequestration of calcium ions that are released upon receipt of a signal relayed by the T tubules from the neuromuscular junction.
	GO:0055119	relaxation of cardiac muscle	The process in which the extent of cardiac muscle contraction is reduced.
	GO:0042178	xenobiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016529	sarcoplasmic reticulum	A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:37 - Pro A:38	[ RasMol ]
		Ala B:37 - Pro B:38	[ RasMol ]
		Arg A:205 - Pro A:206	[ RasMol ]
		Arg B:205 - Pro B:206	[ RasMol ]
		Leu A:59 - Pro A:60	[ RasMol ]
		Leu B:59 - Pro B:60	[ RasMol ]

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	1ykc
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	GSTM2_HUMAN \| P28161
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	2.5.1.18
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UniProtKB/Swiss-Prot
	GSTM2_HUMAN \| P28161	:	1hna 1hnb 1hnc 1xw5 2ab6 2c4j 2gtu 3gtu 3gur

1xw5	STRUCTURE OF HUMAN GLUTATHIONE-S-TRANSFERASE M2-2 COMPLEXED WITH GLUTATHIONE
2gtu	STRUCTURE OF LIGAND-FREE HUMAN GLUTATHIONE-S-TRANSFERASE M2-2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (8, 16)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

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Gene Ontology (24, 24)

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