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(-) Description

Title :  CRYSTAL STRUCTURE OF GAMMA-GLUTAMYLTRANSPEPTIDASE FROM ESCHERICHIA COLI ACYL-ENZYME INTERMEDIATE
 
Authors :  T. Okada, K. Wada, K. Fukuyama
Date :  16 Dec 05  (Deposition) - 18 Apr 06  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Gamma-Glutamyltransferase, Ggt, Gamma-Gtp, Glutathione, Acyl-Enzyme Intermediate, 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  (3, 38)

Asymmetric Unit (3, 38)
No.NameCountTypeFull Name
1GGL2Ligand/IonGAMMA-L-GLUTAMIC ACID
2GOL4Ligand/IonGLYCEROL
3MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 19)
No.NameCountTypeFull Name
1GGL1Ligand/IonGAMMA-L-GLUTAMIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 19)
No.NameCountTypeFull Name
1GGL1Ligand/IonGAMMA-L-GLUTAMIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:114 , THR B:391 , ASN B:411 , GLN B:430 , ASP B:433 , SER B:462 , SER B:463 , MSE B:464 , PRO B:482 , GLY B:483 , GLY B:484 , ILE B:487 , HOH B:1001 , HOH B:1121BINDING SITE FOR RESIDUE GGL B 601
2AC2SOFTWAREARG C:114 , THR D:391 , ASN D:411 , GLN D:430 , ASP D:433 , SER D:462 , SER D:463 , MSE D:464 , GLY D:483 , GLY D:484 , ILE D:487 , HOH D:1002 , HOH D:1023BINDING SITE FOR RESIDUE GGL D 602
3AC3SOFTWAREASP B:574 , ASP B:575 , HOH B:1034 , HOH B:1167 , HOH B:1491 , HOH B:1787BINDING SITE FOR RESIDUE GOL B 701
4AC4SOFTWAREASP D:574 , ASP D:575 , HOH D:1068 , HOH D:1131 , HOH D:1681BINDING SITE FOR RESIDUE GOL D 702
5AC5SOFTWAREGLN C:366 , GLU C:377 , ILE C:378 , ARG C:379 , HOH C:1290 , HOH C:1495 , HOH C:1520BINDING SITE FOR RESIDUE GOL C 703
6AC6SOFTWAREASN A:309 , LYS A:361 , ALA A:364 , ASP A:365BINDING SITE FOR RESIDUE GOL A 704

(-) SS Bonds  (0, 0)

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

(-) 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 2DBW)

(-) 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 2DBW)

(-) 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:359
 aligned with GGT_ECOLI | P18956 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:359
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378         
            GGT_ECOLI    29 APPVSYGVEEDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
               SCOP domains d2dbw.1 A:29-387,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
                 2dbw A  29 APPVSYGVEEDVFHPVRAKQGmVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFmLIRSKNGNTTAIDFREmAPAKATRDmFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTmPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEmIAENGPDEFYKGTIAEQIAQEmQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSmPPPSSGGIHIVQILNILENFDmKKYGFGSADAmQImAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
                                    38        48 |      58        68        78        88        98|      108       118      |128       138       148       158     | 168       178       188       198       208       218       228    |  238       248      |258       268       278       288 |     298       308   |   318    |  328       338       348       358       368       378         
                                                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 d2dbw.1 A:29-387,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....hhhhhhhhhhhh..eee.......eeeee.....eeeee.......eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE G_GLU_TRANSPEPTIDASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dbw 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:356
 aligned with GGT_ECOLI | P18956 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:356
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      
            GGT_ECOLI    32 VSYGVEEDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
               SCOP domains d2dbw.2 C:32-387,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.hhhhhhhhhhhhhhh...hhhhhhhhee..ee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh..eee..eeeee..eeeee.....hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dbw C  32 VSYGVEEDVFHPVRAKQGmVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFmLIRSKNGNTTAIDFREmAPAKATRDmFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTmPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEmIAENGPDEFYKGTIAEQIAQEmQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSmPPPSSGGIHIVQILNILENFDmKKYGFGSADAmQImAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
                                    41        51        61        71        81        91       101       111    |  121   |   131       141       151       161  |    171       181       191       201       211       221       231 |     241       251   |   261       271       281       291       301       311|      321 |  |  331       341       351       361       371       381      
                                             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 d2dbw.2 C:32-387,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
                 2dbw 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 2DBW)

(-) Pfam Domains  (0, 0)

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

(-) 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 2dbx 2dg5 2e0w 2e0x 2e0y 2z8i 2z8j 2z8k 5b5t

(-) Related Entries Specified in the PDB File

2dbu THE SAME PROTEIN
2dbx THE SAME PROTEIN COMPLEXED WITH L-GLUTAMATE