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(-) Description

Title :  CRYSTAL STRUCTURE OF MITOCHONDRIAL CLASS KAPPA GLUTATHIONE TRANSFERASE
 
Authors :  J. E. Ladner, J. F. Parsons, C. L. Rife, G. L. Gilliland, R. N. Armstrong
Date :  08 Oct 03  (Deposition) - 03 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Glutathione-S-Transferase, Glutathione Transferase, Kappa Gst, Rgstk1-1 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. E. Ladner, J. F. Parsons, C. L. Rife, G. L. Gilliland, R. N. Armstrong
Parallel Evolutionary Pathways For Glutathione Transferases: Structure And Mechanism Of The Mitochondrial Class Kappa Enzyme Rgstk1-1
Biochemistry V. 43 352 2004
PubMed-ID: 14717589  |  Reference-DOI: 10.1021/BI035832Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTATHIONE S-TRANSFERASE, MITOCHONDRIAL
    ChainsA, B, C, D
    EC Number2.5.1.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-20B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGSGSTK1-1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGST 13-13, GLUTATHIONE S-TRANSFERASE SUBUNIT 13, GST CLASS-KAPPA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GSH4Ligand/IonGLUTATHIONE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:16 , PRO A:17 , TYR A:18 , ASN A:53 , PHE A:181 , GLY A:182 , LEU A:183 , PHE A:198 , GLY A:199 , SER A:200 , ASP A:201 , LYS B:62 , ARG B:202BINDING SITE FOR RESIDUE GSH A 301
2AC2SOFTWARELYS A:62 , ARG A:202 , SER B:16 , PRO B:17 , TYR B:18 , LEU B:44 , MET B:48 , ASN B:53 , GLY B:182 , LEU B:183 , PHE B:198 , GLY B:199 , SER B:200 , ASP B:201 , HOH B:560 , HOH B:669BINDING SITE FOR RESIDUE GSH B 401
3AC3SOFTWARESER C:16 , PRO C:17 , TYR C:18 , GLY C:182 , LEU C:183 , SER C:200 , ASP C:201 , HOH C:765 , LYS D:62 , ARG D:202BINDING SITE FOR RESIDUE GSH C 801
4AC4SOFTWARELYS C:62 , ARG C:202 , SER D:16 , PRO D:17 , TYR D:18 , MET D:48 , PHE D:181 , GLY D:182 , LEU D:183 , PHE D:198 , GLY D:199 , SER D:200 , ASP D:201 , HOH D:763BINDING SITE FOR RESIDUE GSH D 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R4W)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:183 -Pro A:184
2Leu B:183 -Pro B:184
3Leu C:183 -Pro C:184
4Leu D:183 -Pro D:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R4W)

(-) Exons   (8, 32)

Asymmetric Unit (8, 32)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000222751ENSRNOE00000157423chr4:69999767-69999872106GSTK1_RAT1-24244A:2-24
B:2-24
C:2-24
D:2-24
23
23
23
23
1.2ENSRNOT000000222752ENSRNOE00000157567chr4:70000354-7000043582GSTK1_RAT25-52284A:25-52
B:25-52
C:25-52
D:25-52
28
28
28
28
1.3ENSRNOT000000222753ENSRNOE00000157738chr4:70000620-70000748129GSTK1_RAT52-95444A:52-95
B:52-95
C:52-95
D:52-95
44
44
44
44
1.4ENSRNOT000000222754ENSRNOE00000157901chr4:70001172-70001272101GSTK1_RAT95-128344A:95-128
B:95-128
C:95-128
D:95-128
34
34
34
34
1.5ENSRNOT000000222755ENSRNOE00000158062chr4:70001419-7000145436GSTK1_RAT129-140124A:129-140
B:129-140
C:129-140
D:129-140
12
12
12
12
1.6ENSRNOT000000222756ENSRNOE00000158223chr4:70003032-70003148117GSTK1_RAT141-179394A:141-179
B:141-179
C:141-179
D:141-179
39
39
39
39
1.7ENSRNOT000000222757ENSRNOE00000158370chr4:70003483-7000357694GSTK1_RAT180-211324A:180-211
B:180-211
C:180-211
D:180-211
32
32
32
32
1.8ENSRNOT000000222758ENSRNOE00000232407chr4:70003855-70004086232GSTK1_RAT211-226164A:211-222
B:211-222
C:211-222
D:211-222
12
12
12
12

(-) 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:221
 aligned with GSTK1_RAT | P24473 from UniProtKB/Swiss-Prot  Length:226

    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 
            GSTK1_RAT     2 GPAPRVLELFYDVLSPYSWLGFEVLCRYQHLWNIKLKLRPALLAGIMKDSGNQPPAMVPHKGQYILKEIPLLKQLFQVPMSVPKDFFGEHVKKGTVNAMRFLTAVSMEQPEMLEKVSRELWMRIWSRDEDITESQNILSAAEKAGMATAQAQHLLNKISTELVKSKLRETTGAACKYGAFGLPTTVAHVDGKTYMLFGSDRMELLAYLLGEKWMGPVPPTL 222
               SCOP domains d1r4wa_ A: Mitochondrial class kappa glutathione S-transferase                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh......eeeeee..eeeeee...hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:2-24  Exon 1.2  PDB: A:25-52      ------------------------------------------Exon 1.4  PDB: A:95-128           Exon 1.5    Exon 1.6  PDB: A:141-179               Exon 1.7  PDB: A:180-211        ----------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.3  PDB: A:52-95 UniProt: 52-95       -------------------------------------------------------------------------------------------------------------------Exon 1.8     Transcript 1 (2)
                 1r4w A   2 GPAPRVLELFYDVLSPYSWLGFEVLCRYQHLWNIKLKLRPALLAGIMKDSGNQPPAMVPHKGQYILKEIPLLKQLFQVPMSVPKDFFGEHVKKGTVNAMRFLTAVSMEQPEMLEKVSRELWMRIWSRDEDITESQNILSAAEKAGMATAQAQHLLNKISTELVKSKLRETTGAACKYGAFGLPTTVAHVDGKTYMLFGSDRMELLAYLLGEKWMGPVPPTL 222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with GSTK1_RAT | P24473 from UniProtKB/Swiss-Prot  Length:226

    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 
            GSTK1_RAT     2 GPAPRVLELFYDVLSPYSWLGFEVLCRYQHLWNIKLKLRPALLAGIMKDSGNQPPAMVPHKGQYILKEIPLLKQLFQVPMSVPKDFFGEHVKKGTVNAMRFLTAVSMEQPEMLEKVSRELWMRIWSRDEDITESQNILSAAEKAGMATAQAQHLLNKISTELVKSKLRETTGAACKYGAFGLPTTVAHVDGKTYMLFGSDRMELLAYLLGEKWMGPVPPTL 222
               SCOP domains d1r4wb_ B: Mitochondrial class kappa glutathione S-transferase                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhhhhhhhhhhhh....eeeeeee.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh......eeeeee..eeeeee...hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:2-24  Exon 1.2  PDB: B:25-52      ------------------------------------------Exon 1.4  PDB: B:95-128           Exon 1.5    Exon 1.6  PDB: B:141-179               Exon 1.7  PDB: B:180-211        ----------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.3  PDB: B:52-95 UniProt: 52-95       -------------------------------------------------------------------------------------------------------------------Exon 1.8     Transcript 1 (2)
                 1r4w B   2 GPAPRVLELFYDVLSPYSWLGFEVLCRYQHLWNIKLKLRPALLAGIMKDSGNQPPAMVPHKGQYILKEIPLLKQLFQVPMSVPKDFFGEHVKKGTVNAMRFLTAVSMEQPEMLEKVSRELWMRIWSRDEDITESQNILSAAEKAGMATAQAQHLLNKISTELVKSKLRETTGAACKYGAFGLPTTVAHVDGKTYMLFGSDRMELLAYLLGEKWMGPVPPTL 222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 

Chain C from PDB  Type:PROTEIN  Length:221
 aligned with GSTK1_RAT | P24473 from UniProtKB/Swiss-Prot  Length:226

    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 
            GSTK1_RAT     2 GPAPRVLELFYDVLSPYSWLGFEVLCRYQHLWNIKLKLRPALLAGIMKDSGNQPPAMVPHKGQYILKEIPLLKQLFQVPMSVPKDFFGEHVKKGTVNAMRFLTAVSMEQPEMLEKVSRELWMRIWSRDEDITESQNILSAAEKAGMATAQAQHLLNKISTELVKSKLRETTGAACKYGAFGLPTTVAHVDGKTYMLFGSDRMELLAYLLGEKWMGPVPPTL 222
               SCOP domains d1r4wc_ C: Mitochondrial class kappa glutathione S-transferase                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..eeeeee...hhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: C:2-24  Exon 1.2  PDB: C:25-52      ------------------------------------------Exon 1.4  PDB: C:95-128           Exon 1.5    Exon 1.6  PDB: C:141-179               Exon 1.7  PDB: C:180-211        ----------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.3  PDB: C:52-95 UniProt: 52-95       -------------------------------------------------------------------------------------------------------------------Exon 1.8     Transcript 1 (2)
                 1r4w C   2 GPAPRVLELFYDVLSPYSWLGFEVLCRYQHLWNIKLKLRPALLAGIMKDSGNQPPAMVPHKGQYILKEIPLLKQLFQVPMSVPKDFFGEHVKKGTVNAMRFLTAVSMEQPEMLEKVSRELWMRIWSRDEDITESQNILSAAEKAGMATAQAQHLLNKISTELVKSKLRETTGAACKYGAFGLPTTVAHVDGKTYMLFGSDRMELLAYLLGEKWMGPVPPTL 222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 

Chain D from PDB  Type:PROTEIN  Length:221
 aligned with GSTK1_RAT | P24473 from UniProtKB/Swiss-Prot  Length:226

    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 
            GSTK1_RAT     2 GPAPRVLELFYDVLSPYSWLGFEVLCRYQHLWNIKLKLRPALLAGIMKDSGNQPPAMVPHKGQYILKEIPLLKQLFQVPMSVPKDFFGEHVKKGTVNAMRFLTAVSMEQPEMLEKVSRELWMRIWSRDEDITESQNILSAAEKAGMATAQAQHLLNKISTELVKSKLRETTGAACKYGAFGLPTTVAHVDGKTYMLFGSDRMELLAYLLGEKWMGPVPPTL 222
               SCOP domains d1r4wd_ D: Mitochondrial class kappa glutathione S-transferase                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----DSBA-1r4wD01 D:7-211                                                                                                                                                                                         ----------- Pfam domains (1)
           Pfam domains (2) -----DSBA-1r4wD02 D:7-211                                                                                                                                                                                         ----------- Pfam domains (2)
           Pfam domains (3) -----DSBA-1r4wD03 D:7-211                                                                                                                                                                                         ----------- Pfam domains (3)
           Pfam domains (4) -----DSBA-1r4wD04 D:7-211                                                                                                                                                                                         ----------- Pfam domains (4)
         Sec.struct. author ....eeeeeee...hhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh......eeeeee..eeeeee...hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: D:2-24  Exon 1.2  PDB: D:25-52      ------------------------------------------Exon 1.4  PDB: D:95-128           Exon 1.5    Exon 1.6  PDB: D:141-179               Exon 1.7  PDB: D:180-211        ----------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.3  PDB: D:52-95 UniProt: 52-95       -------------------------------------------------------------------------------------------------------------------Exon 1.8     Transcript 1 (2)
                 1r4w D   2 GPAPRVLELFYDVLSPYSWLGFEVLCRYQHLWNIKLKLRPALLAGIMKDSGNQPPAMVPHKGQYILKEIPLLKQLFQVPMSVPKDFFGEHVKKGTVNAMRFLTAVSMEQPEMLEKVSRELWMRIWSRDEDITESQNILSAAEKAGMATAQAQHLLNKISTELVKSKLRETTGAACKYGAFGLPTTVAHVDGKTYMLFGSDRMELLAYLLGEKWMGPVPPTL 222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R4W)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GSTK1_RAT | P24473)
molecular function
    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:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
    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:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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: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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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