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(-) Description

Title :  CRYSTAL STRUCTURE OF GAMMA-GLUTAMYL TRANSPEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH HYDROLYZED GLUTATHIONE
 
Authors :  T. Okada, K. Wada, K. Fukuyama
Date :  08 Mar 06  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Gamma-Glutamyltransferase, Ggt, Gamma-Gt, Glutathione, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Okada, H. Suzuki, K. Wada, H. Kumagai, K. Fukuyama
Crystal Structures Of Gamma-Glutamyltranspeptidase From Escherichia Coli, A Key Enzyme In Glutathione Metabolism, And Its Reaction Intermediate.
Proc. Natl. Acad. Sci. Usa V. 103 6471 2006
PubMed-ID: 16618936  |  Reference-DOI: 10.1073/PNAS.0511020103

(-) Compounds

Molecule 1 - GAMMA-GLUTAMYLTRANSPEPTIDASE
    ChainsA, C
    EC Number2.3.2.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSH1291
    Expression System StrainSH1603
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentLARGE SUBUNIT
    GeneGGT
    Organism ScientificESCHERICHIA COLI K12
    Organism Taxid83333
    StrainK-12
 
Molecule 2 - GAMMA-GLUTAMYLTRANSPEPTIDASE
    ChainsB, D
    EC Number2.3.2.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSH1291
    Expression System StrainSH1603
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSMALL SUBUNIT
    GeneGGT
    Organism ScientificESCHERICHIA COLI K12
    Organism Taxid83333
    StrainK-12

 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  (4, 37)

Asymmetric Unit (4, 37)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GLU2Mod. Amino AcidGLUTAMIC ACID
3GOL1Ligand/IonGLYCEROL
4MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GOL1Ligand/IonGLYCEROL
4MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 17)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GOL-1Ligand/IonGLYCEROL
4MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:569 , SER B:572 , ASP B:575 , HOH B:1860 , HOH B:1861 , HOH B:1862 , HOH B:1863BINDING SITE FOR RESIDUE CA B 701
2AC2SOFTWAREASP D:569 , SER D:572 , ASP D:575 , HOH D:1864 , HOH D:1865 , HOH D:1866 , HOH D:1867BINDING SITE FOR RESIDUE CA D 702
3AC3SOFTWAREARG A:114 , THR B:391 , ASN B:411 , GLN B:430 , ASP B:433 , TYR B:444 , SER B:462 , SER B:463 , MSE B:464 , GLY B:483 , GLY B:484 , HOH B:1067BINDING SITE FOR RESIDUE GLU B 601
4AC4SOFTWAREARG C:114 , THR D:391 , ASN D:411 , GLN D:430 , ASP D:433 , TYR D:444 , SER D:462 , SER D:463 , MSE D:464 , GLY D:483 , GLY D:484 , HOH D:1058 , HOH D:1669BINDING SITE FOR RESIDUE GLU D 602
5AC5SOFTWAREGLN A:366 , GLU A:377 , ILE A:378 , ARG A:379 , HOH A:1074 , HOH A:1524 , HOH A:1540 , HOH A:1623BINDING SITE FOR RESIDUE GOL A 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DG5)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:292 -Pro A:293
2Leu B:519 -Pro B:520
3Pro C:292 -Pro C:293
4Leu D:519 -Pro D:520

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DG5)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GLU_TRANSPEPTIDASEPS00462 Gamma-glutamyltranspeptidase signature.GGT_ECOLI391-415
 
  2B:391-415
D:391-415
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GLU_TRANSPEPTIDASEPS00462 Gamma-glutamyltranspeptidase signature.GGT_ECOLI391-415
 
  1B:391-415
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GLU_TRANSPEPTIDASEPS00462 Gamma-glutamyltranspeptidase signature.GGT_ECOLI391-415
 
  1-
D:391-415

(-) Exons   (0, 0)

(no "Exon" information available for 2DG5)

(-) 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:351
 aligned with GGT_ECOLI | P18956 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:351
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386 
            GGT_ECOLI    37 EEDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
               SCOP domains d2dg5.1 A:37-387,B:391-580 Gamma-glutamyltranspeptidase, GGT                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...eeee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeeee.....eeeeee....................hhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhhhhhhhhhhhhee..ee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh..eee..eeeee..eeeee.....hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dg5 A  37 EEDVFHPVRAKQGmVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFmLIRSKNGNTTAIDFREmAPAKATRDmFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTmPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEmIAENGPDEFYKGTIAEQIAQEmQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSmPPPSSGGIHIVQILNILENFDmKKYGFGSADAmQImAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
                                    46   |    56        66        76        86        96  |    106       116       126       136       146       156       166       176       186       196       206       216       226      |236       246       256       266       276       286   |   296       306     | 316      |326       336       346       356       366       376       386 
                                        50-MSE                                           99-MSE          116-MSE  125-MSE                                164-MSE                                                              233-MSE               255-MSE                            290-MSE               312-MSE    323-MSE                                                            
                                                                                                                                                                                                                                                                                                                           326-MSE                                                         

Chain B from PDB  Type:PROTEIN  Length:190
 aligned with GGT_ECOLI | P18956 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:190
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580
            GGT_ECOLI   391 TTHYSVVDKDGNAVAVTYTLNTTFGTGIVAGESGILLNNQMDDFSAKPGVPNVYGLVGGDANAVGPNKRPLSSMSPTIVVKDGKTWLVTGSPGGSRIITTVLQMVVNSIDYGLNVAEATNAPRFHHQWLPDELRVEKGFSPDTLKLLEAKGQKVALKEAMGSTQSIMVGPDGELYGASDPRSVDDLTAGY 580
               SCOP domains d2dg5.1 A:37-387,B:391-580 Gamma-glutamyltranspeptidase, GGT                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee..........hhhhh....hhhhhh................................eeeee..eeeeee...hhhhhhhhhhhhhhhhhh...hhhhhhhh..ee.......eee....hhhhhhhhhhh...eee.......eeeee.....eeeee.......eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE G_GLU_TRANSPEPTIDASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dg5 B 391 TTHYSVVDKDGNAVAVTYTLNTTFGTGIVAGESGILLNNQmDDFSAKPGVPNVYGLVGGDANAVGPNKRPLSSmSPTIVVKDGKTWLVTGSPGGSRIITTVLQmVVNSIDYGLNVAEATNAPRFHHQWLPDELRVEKGFSPDTLKLLEAKGQKVALKEAmGSTQSImVGPDGELYGASDPRSVDDLTAGY 580
                                   400       410       420       430|      440       450       460   |   470       480       490   |   500       510       520       530       540       550      |560       570       580
                                                                  431-MSE                          464-MSE                       494-MSE                                                 550-MSE  |                       
                                                                                                                                                                                                557-MSE                   

Chain C from PDB  Type:PROTEIN  Length:351
 aligned with GGT_ECOLI | P18956 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:351
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386 
            GGT_ECOLI    37 EEDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
               SCOP domains d2dg5.2 C:37-387,D:391-580 Gamma-glutamyltranspeptidase, GGT                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eeeee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeeee.....eeeeee....................hhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhhhhhhhhhhhhee..ee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh..eee..eeeee..eeeee.....hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dg5 C  37 EEDVFHPVRAKQGmVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFmLIRSKNGNTTAIDFREmAPAKATRDmFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTmPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEmIAENGPDEFYKGTIAEQIAQEmQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSmPPPSSGGIHIVQILNILENFDmKKYGFGSADAmQImAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
                                    46   |    56        66        76        86        96  |    106       116       126       136       146       156       166       176       186       196       206       216       226      |236       246       256       266       276       286   |   296       306     | 316      |326       336       346       356       366       376       386 
                                        50-MSE                                           99-MSE          116-MSE  125-MSE                                164-MSE                                                              233-MSE               255-MSE                            290-MSE               312-MSE    323-MSE                                                            
                                                                                                                                                                                                                                                                                                                           326-MSE                                                         

Chain D from PDB  Type:PROTEIN  Length:190
 aligned with GGT_ECOLI | P18956 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:190
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580
            GGT_ECOLI   391 TTHYSVVDKDGNAVAVTYTLNTTFGTGIVAGESGILLNNQMDDFSAKPGVPNVYGLVGGDANAVGPNKRPLSSMSPTIVVKDGKTWLVTGSPGGSRIITTVLQMVVNSIDYGLNVAEATNAPRFHHQWLPDELRVEKGFSPDTLKLLEAKGQKVALKEAMGSTQSIMVGPDGELYGASDPRSVDDLTAGY 580
               SCOP domains d2dg5.2 C:37-387,D:391-580 Gamma-glutamyltranspeptidase, GGT                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee..........hhhhh....hhhhhh................................eeeee..eeeeee...hhhhhhhhhhhhhhhhhh...hhhhhhhh..ee.......eee....hhhhhhhhhhh...eee.......eeeee.....eeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE G_GLU_TRANSPEPTIDASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dg5 D 391 TTHYSVVDKDGNAVAVTYTLNTTFGTGIVAGESGILLNNQmDDFSAKPGVPNVYGLVGGDANAVGPNKRPLSSmSPTIVVKDGKTWLVTGSPGGSRIITTVLQmVVNSIDYGLNVAEATNAPRFHHQWLPDELRVEKGFSPDTLKLLEAKGQKVALKEAmGSTQSImVGPDGELYGASDPRSVDDLTAGY 580
                                   400       410       420       430|      440       450       460   |   470       480       490   |   500       510       520       530       540       550      |560       570       580
                                                                  431-MSE                          464-MSE                       494-MSE                                                 550-MSE  |                       
                                                                                                                                                                                                557-MSE                   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DG5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DG5)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GGT_ECOLI | P18956)
molecular function
    GO:0036374    glutathione hydrolase activity    Catalysis of the reaction: glutathione + H2O = L-cysteinylglycine + L-glutamate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003840    obsolete gamma-glutamyltransferase activity    OBSOLETE. Catalysis of the reaction: (5-L-glutamyl)-peptide + an amino acid = peptide + 5-L-glutamyl-amino acid.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006750    glutathione biosynthetic process    The chemical reactions and pathways resulting in the formation of 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.
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GGT_ECOLI | P189562dbu 2dbw 2dbx 2e0w 2e0x 2e0y 2z8i 2z8j 2z8k 5b5t

(-) Related Entries Specified in the PDB File

2dbu THE SAME PROTEIN
2dbw THE SAME PROTEIN, ACYL-ENZYME INTERMEDIATE
2dbx THE SAME PROTEIN COMPLEXED WITH L-GLUTAMATE