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(-) Description

Title :  CRYSTAL STRUCTURE OF BOMBYX MORI SIGMA-CLASS GLUTATHIONE TRANSFERASE IN COMPLEX WITH GLUTATHIONE
 
Authors :  K. Yamamoto, A. Higashiura, A. Nakagawa, M. Suzuki
Date :  08 Mar 12  (Deposition) - 06 Mar 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Alpha/Beta-Barrel, Transferase, Glutathione (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yamamoto, A. Higashiura, M. Suzuki, K. Aritake, Y. Urade, N. Uodome A. Nakagawa
Crystal Structure Of A Bombyx Mori Sigma-Class Glutathione Transferase Exhibiting Prostaglandin E Synthase Activity
Biochim. Biophys. Acta V. 1830 3711 2013
PubMed-ID: 23458683  |  Reference-DOI: 10.1016/J.BBAGEN.2013.02.021

(-) Compounds

Molecule 1 - GLUTATHIONE S-TRANSFERASE SIGMA
    Chains: A
    EC Number: 2.5.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GST SIGMA
    Organism Common: SILK MOTH
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2GSH1Ligand/IonGLUTATHIONE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO10Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (4, 26)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2GSH2Ligand/IonGLUTATHIONE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO20Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (4, 13)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2GSH1Ligand/IonGLUTATHIONE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO10Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:8 , PHE A:9 , LEU A:14 , TRP A:39 , LYS A:43 , GLN A:50 , MET A:51 , PRO A:52 , GLN A:63 , SER A:64 , GLU A:93 , ASP A:97 , PGO A:305 , HOH A:407 , HOH A:463BINDING SITE FOR RESIDUE GSH A 301
02AC2SOFTWARETYR A:75 , ASP A:171 , GLN A:174BINDING SITE FOR RESIDUE PGO A 302
03AC3SOFTWAREPRO A:47 , PHE A:48 , GLN A:90 , GLU A:135 , LYS A:139 , HOH A:409 , HOH A:425BINDING SITE FOR RESIDUE PGO A 303
04AC4SOFTWAREPRO A:44 , LYS A:45 , THR A:46 , GLU A:135 , PGO A:309BINDING SITE FOR RESIDUE PGO A 304
05AC5SOFTWAREGLU A:93 , ASN A:96 , ASP A:97 , ARG A:99 , GSH A:301 , HOH A:419 , HOH A:463BINDING SITE FOR RESIDUE PGO A 305
06AC6SOFTWARESER A:101 , LYS A:125BINDING SITE FOR RESIDUE PEG A 306
07AC7SOFTWAREHOH A:428BINDING SITE FOR RESIDUE PGO A 307
08AC8SOFTWAREASN A:81 , GLU A:84 , ARG A:180 , ILE A:183 , GLU A:184 , LEU A:187BINDING SITE FOR RESIDUE PGO A 308
09AC9SOFTWARELYS A:43 , THR A:46 , PRO A:47 , PHE A:48 , GLY A:49 , LYS A:132 , PGO A:304 , HOH A:448BINDING SITE FOR RESIDUE PGO A 309
10BC1SOFTWAREPRO A:2 , GLN A:27 , LYS A:74 , TYR A:75BINDING SITE FOR RESIDUE PGO A 310
11BC2SOFTWAREASN A:141 , LYS A:181 , ALA A:185 , GLU A:203 , 1PE A:313BINDING SITE FOR RESIDUE PGO A 311
12BC3SOFTWARELYS A:12 , ASP A:161BINDING SITE FOR RESIDUE PGO A 312
13BC4SOFTWAREASN A:141 , GLY A:142 , ALA A:178 , LYS A:181 , PGO A:311 , HOH A:459BINDING SITE FOR RESIDUE 1PE A 313

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VPQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met A:51 -Pro A:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VPQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VPQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3VPQ)

(-) 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:203
 aligned with Q5CCJ4_BOMMO | Q5CCJ4 from UniProtKB/TrEMBL  Length:204

    Alignment length:203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   
         Q5CCJ4_BOMMO     2 PNVKFYYFPVKALGESQRLLLAYGGQEFEDNRISSENWPEFKPKTPFGQMPVLEIDGKQYAQSTAICRYLGRKYGLAGANDEEAFEIDQNVEFLNDIRASAASVHYEKDEAVKAKKKAELEETKYPFFFEKLNEILTKNNGHIALGKLTWGDFVYAGMYDYLKAMLQKPDLEQKYPAFRKPIEAVLAIPKVKAYVDAAPRTEL 204
               SCOP domains d3vpqa1 A:2-76 automated matches                                           d3vpqa2 A:77-204 automated matches                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhh....eeee....hhhhhhhhh......eeee..eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpq A   2 PNVKFYYFPVKALGESQRLLLAYGGQEFEDNRISSENWPEFKPKTPFGQMPVLEIDGKQYAQSTAICRYLGRKYGLAGANDEEAFEIDQNVEFLNDIRASAASVHYEKDEAVKAKKKAELEETKYPFFFEKLNEILTKNNGHIALGKLTWGDFVYAGMYDYLKAMLQKPDLEQKYPAFRKPIEAVLAIPKVKAYVDAAPRTEL 204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VPQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VPQ)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5CCJ4_BOMMO | Q5CCJ4)
molecular 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.

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 Related Entries

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        Q5CCJ4_BOMMO | Q5CCJ4: 3vpt 3vur

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