1PL2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE TRANSFERASE (GST) A1-1 T68E MUTANT IN COMPLEX WITH DECARBOXY-GLUTATHIONE

Authors :   E. Grahn, E. Jakobsson, A. Gustafsson, L. Grehn, B. Olin, M. Wahlberg, D. Madsen, G. J. Kleywegt, B. Mannervik

Date :   06 Jun 03 (Deposition) - 22 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Domain1:Alpha-Beta, Domain2: Alpha-Helical, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Grahn, M. Novotny, E. Jakobsson, A. Gustafsson, L. Grehn, B. Olin, D. Madsen, M. Wahlberg, B. Mannervik, G. J. Kleywegt
New Crystal Structures Of Human Glutathione Transferase A1-1 Shed Light On Glutathione Binding And The Conformation Of The C-Terminal Helix.
Acta Crystallogr. , Sect. D V. 62 197 2006
PubMed-ID: 16421451 | Reference-DOI: 10.1107/S0907444905039296
(for further references see the PDB file header)

Molecule 1 - GLUTATHIONE S-TRANSFERASE A1
	Chains	:	A, B
	EC Number	:	2.5.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GTH1, HA SUBUNIT 1, GST-EPSILON, GSTA1-1, GST CLASS-ALPHA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ABY	2	Ligand/Ion	N-(4-AMINOBUTANOYL)-S-(4-METHOXYBENZYL)-L-CYSTEINYLGLYCINE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO B:56 , GLU B:68 , ABY B:655 , HOH B:676	BINDING SITE FOR RESIDUE CL B 601
2	AC2	SOFTWARE	PRO A:56 , GLU A:68 , ABY A:654	BINDING SITE FOR RESIDUE CL A 602
3	AC3	SOFTWARE	TYR A:9 , ARG A:45 , GLN A:54 , VAL A:55 , GLN A:67 , LEU A:107 , VAL A:111 , MET A:208 , PHE A:220 , CL A:602 , HOH A:806 , HOH A:880 , ASP B:101 , ARG B:131	BINDING SITE FOR RESIDUE ABY A 654
4	AC4	SOFTWARE	ASP A:101 , ARG A:131 , TYR B:9 , ARG B:45 , GLN B:54 , VAL B:55 , GLN B:67 , LEU B:107 , VAL B:111 , MET B:208 , PHE B:220 , CL B:601 , HOH B:828	BINDING SITE FOR RESIDUE ABY B 655

(no "SS Bond" information available for 1PL2)

Asymmetric/Biological Unit

No.	Residues
1	Val A:55	-	Pro A:56
2	Val B:55	-	Pro B:56

Asymmetric/Biological Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033978	T	19	I	GSTA1_HUMAN	Polymorphism	1051578	A/B	T	19	I
2	UniProt	VAR_049482	P	113	Q	GSTA1_HUMAN	Polymorphism	1051745	A/B	P	113	Q
3	UniProt	VAR_049483	K	117	Q	GSTA1_HUMAN	Polymorphism	1051757	A/B	K	117	Q

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GST_NTER	PS50404	Soluble glutathione S-transferase N-terminal domain profile.	GSTA1_HUMAN	3-83	2	A:3-83 B:3-83
2	GST_CTER	PS50405	Soluble glutathione S-transferase C-terminal domain profile.	GSTA1_HUMAN	85-207	2	A:85-207 B:85-207

Asymmetric/Biological Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000334575	1a	ENSE00002201258	chr6:52668708-52668583	126	GSTA1_HUMAN	-	0	0	-	-
1.2	ENST00000334575	2	ENSE00002162073	chr6:52664095-52663979	117	GSTA1_HUMAN	1-29	29	2	A:2-29 B:2-29	28 28
1.3	ENST00000334575	3	ENSE00002190926	chr6:52662435-52662384	52	GSTA1_HUMAN	30-47	18	2	A:30-47 B:30-47	18 18
1.4	ENST00000334575	4	ENSE00002186617	chr6:52661112-52660980	133	GSTA1_HUMAN	47-91	45	2	A:47-91 B:47-91	45 45
1.5b	ENST00000334575	5b	ENSE00002141355	chr6:52659064-52658923	142	GSTA1_HUMAN	91-138	48	2	A:91-138 B:91-138	48 48
1.6	ENST00000334575	6	ENSE00002159902	chr6:52657785-52657654	132	GSTA1_HUMAN	139-182	44	2	A:139-182 B:139-182	44 44
1.7	ENST00000334575	7	ENSE00002170665	chr6:52656778-52656462	317	GSTA1_HUMAN	183-222	40	2	A:183-222 B:183-222	40 40

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:221
 aligned with GSTA1_HUMAN | P08263 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
          GSTA1_HUMAN     2 AEKPKLHYFNARGRMESTRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQTRAILNYIASKYNLYGKDIKERALIDMYIEGIADLGEMILLLPVCPPEEKDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEEARKIFRF 222
               SCOP domains d1pl2a2 A:2-80 Class alpha GST                                                 d1pl2a1 A:81-222 Class alpha GST                                                                                                               SCOP domains
               CATH domains 1pl2A01 A:2-81,A:191-209 Glutaredoxin                                           1pl2A02 A:82-190  [code=1.20.1050.10, no name defined]                                                       1pl2A01            ------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhhhhhhhhhhh....eeee..hhhhhhhhhhh.........eeee..eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------I---------------------------------------------------------------------------------------------Q---Q--------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GST_NTER  PDB: A:3-83 UniProt: 3-83                                              -GST_CTER  PDB: A:85-207 UniProt: 85-207                                                                                    --------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:2-29       Exon 1.3          -------------------------------------------Exon 1.5b  PDB: A:91-138 UniProt: 91-138        Exon 1.6  PDB: A:139-182 UniProt: 139-182   Exon 1.7  PDB: A:183-222                 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.4  PDB: A:47-91 UniProt: 47-91        ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1pl2 A   2 AEKPKLHYFNARGRMESTRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQERAILNYIASKYNLYGKDIKERALIDMYIEGIADLGEMILLLPVcPPEEKDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEEARKIFRF 222
                                    11        21        31        41        51        61        71        81        91       101       111|      121       131       141       151       161       171       181       191       201       211       221 
                                                                                                                                        112-CSO

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with GSTA1_HUMAN | P08263 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
          GSTA1_HUMAN     2 AEKPKLHYFNARGRMESTRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQTRAILNYIASKYNLYGKDIKERALIDMYIEGIADLGEMILLLPVCPPEEKDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEEARKIFRF 222
               SCOP domains d1pl2b2 B:2-80 Class alpha GST                                                 d1pl2b1 B:81-222 Class alpha GST                                                                                                               SCOP domains
               CATH domains 1pl2B01 B:2-81,B:191-209 Glutaredoxin                                           1pl2B02 B:82-190  [code=1.20.1050.10, no name defined]                                                       1pl2B01            ------------- CATH domains
           Pfam domains (1) ---GST_N-1pl2B03 B:5-77                                                     ---------------------GST_C-1pl2B01 B:99-192                                                                        ------------------------------ Pfam domains (1)
           Pfam domains (2) ---GST_N-1pl2B04 B:5-77                                                     ---------------------GST_C-1pl2B02 B:99-192                                                                        ------------------------------ Pfam domains (2)
         Sec.struct. author ....eeee...hhhhhhhhhhhhhh....eeee..hhhhhhhhhhh.........eeee..eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------I---------------------------------------------------------------------------------------------Q---Q--------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GST_NTER  PDB: B:3-83 UniProt: 3-83                                              -GST_CTER  PDB: B:85-207 UniProt: 85-207                                                                                    --------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:2-29       Exon 1.3          -------------------------------------------Exon 1.5b  PDB: B:91-138 UniProt: 91-138        Exon 1.6  PDB: B:139-182 UniProt: 139-182   Exon 1.7  PDB: B:183-222                 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.4  PDB: B:47-91 UniProt: 47-91        ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1pl2 B   2 AEKPKLHYFNARGRMESTRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQERAILNYIASKYNLYGKDIKERALIDMYIEGIADLGEMILLLPVcPPEEKDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEEARKIFRF 222
                                    11        21        31        41        51        61        71        81        91       101       111|      121       131       141       151       161       171       181       191       201       211       221 
                                                                                                                                        112-CSO

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(

)

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	1pl2A01	A:2-81,A:191-209
1b	1pl2B01	B:2-81,B:191-209

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	1pl2A02	A:82-190
2b	1pl2B02	B:82-190

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GST_C (118)

Family: GST_C (102)

Homo sapiens (Human) (47)

1a	GST_C-1pl2B01	B:99-192
1b	GST_C-1pl2B02	B:99-192

Clan: Thioredoxin (367)

Family: GST_N (88)

Homo sapiens (Human) (45)

2a	GST_N-1pl2B03	B:5-77
2b	GST_N-1pl2B04	B:5-77

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GSTA1_HUMAN | P08263)

molecular function
	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: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:0030855	epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
	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.
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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ABY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CSO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Val A:55 - Pro A:56	[ RasMol ]
		Val B:55 - Pro B:56	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1pl2
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GSTA1_HUMAN \| P08263
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.5.1.18
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GSTA1_HUMAN \| P08263
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1pkw	CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE TRANSFERASE A1-1 IN COMPLEX WITH GLUTATHIONE
1pkz	CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE TRANSFERASE A1-1 COMPLEXED WITH 2-HYDROXYETHYL DISULFIDE
1pl1	CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE TRANSFERASE A1-1 IN COMPLEX WITH A DECARBOXY-GLUTATHIONE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (2, 4)

Exons (6, 12)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File