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(-) Description

Title :  CRYSTAL STRUCTURE OF BOMBYX MORI SIGMA-CLASS GLUTATHIONE TRANSFERASE IN APO FORM
 
Authors :  K. Yamamoto, A. Higashiura, M. Suzuki, A. Nakagawa
Date :  13 Mar 12  (Deposition) - 06 Mar 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Gsh Binding, Cytosol (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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3PGO6Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (3, 22)
No.NameCountTypeFull Name
1PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
2PG42Ligand/IonTETRAETHYLENE GLYCOL
3PGO12Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:43 , THR A:45 , PRO A:46 , PHE A:47 , GLY A:48 , LYS A:131BINDING SITE FOR RESIDUE PGO A 301
02AC2SOFTWARELYS A:11 , ALA A:156BINDING SITE FOR RESIDUE PGO A 302
03AC3SOFTWARETYR A:6 , LYS A:44 , GLU A:54 , GLN A:59BINDING SITE FOR RESIDUE PGO A 303
04AC4SOFTWAREARG A:72 , ASP A:81BINDING SITE FOR RESIDUE PGO A 304
05AC5SOFTWAREGLU A:122 , THR A:123 , GLU A:130 , LYS A:174 , TYR A:175BINDING SITE FOR RESIDUE PEG A 305
06AC6SOFTWARELYS A:180BINDING SITE FOR RESIDUE PEG A 306
07AC7SOFTWAREGLU A:86 , ASN A:90 , GLU A:134 , LYS A:138 , ASN A:139 , ARG A:200BINDING SITE FOR RESIDUE PEG A 307
08AC8SOFTWAREGLY A:75 , LEU A:76 , ALA A:77 , GLY A:78 , LEU A:148 , GLU A:172BINDING SITE FOR RESIDUE PGO A 308
09AC9SOFTWARETHR A:64 , ASN A:95 , ARG A:98 , HOH A:436 , HOH A:449BINDING SITE FOR RESIDUE PGO A 309
10BC1SOFTWAREGLN A:49 , SER A:100 , LYS A:124BINDING SITE FOR RESIDUE PG4 A 310
11BC2SOFTWAREPRO A:9 , VAL A:10 , ASN A:140BINDING SITE FOR RESIDUE PEG A 311

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met A:50 -Pro A:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VPT)

(-) 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 d3vpta1 A:1-75 automated matches                                           d3vpta2 A:76-203 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
                 3vpt A   1 PNVKFYYFPVKALGESQRLLLAYGGQEFEDNRISSENWPEFKPKTPFGQMPVLEIDGKQYAQSTAICRYLGRKYGLAGANDEEAFEIDQNVEFLNDIRASAASVHYEKDEAVKAKKKAELEETKYPFFFEKLNEILTKNNGHIALGKLTWGDFVYAGMYDYLKAMLQKPDLEQKYPAFRKPIEAVLAIPKVKAYVDAAPRTEL 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
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  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 3VPT)

(-) Pfam Domains  (0, 0)

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

(-) 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: 3vpq 3vur

(-) Related Entries Specified in the PDB File

3vpq 3vpu