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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI GAMMA-GLUTAMYLTRANSPEPTIDASE IN COMPLEX WITH ACIVICIN
 
Authors :  K. Wada, M. Irie, K. Fukuyama
Date :  05 Sep 07  (Deposition) - 24 Jun 08  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Acivicin Formed A Covalent Bond With Thr391, Acyltransferase, Glutathione Biosynthesis, Transferase, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Wada, J. Hiratake, M. Irie, T. Okada, C. Yamada, H. Kumagai, H. Suzuki, K. Fukuyama
Crystal Structures Of Escherichia Coli Gamma-Glutamyltranspeptidase In Complex With Azaserine And Acivicin: Novel Mechanistic Implication For Inhibition By Glutamine Antagonists
J. Mol. Biol. V. 380 361 2008
PubMed-ID: 18555071  |  Reference-DOI: 10.1016/J.JMB.2008.05.007

(-) Compounds

Molecule 1 - GAMMA-GLUTAMYLTRANSPEPTIDASE
    Chains: A, C
    EC Number: 2.3.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSH253
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LARGE CHAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: K-12
 
Molecule 2 - GAMMA-GLUTAMYLTRANSPEPTIDASE
    Chains: B, D
    EC Number: 2.3.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSH253
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SMALL CHAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: K-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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1AVN2Ligand/Ion(2S)-AMINO[(5S)-3-CHLORO-4,5-DIHYDROISOXAZOL-5-YL]ACETIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AVN1Ligand/Ion(2S)-AMINO[(5S)-3-CHLORO-4,5-DIHYDROISOXAZOL-5-YL]ACETIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AVN1Ligand/Ion(2S)-AMINO[(5S)-3-CHLORO-4,5-DIHYDROISOXAZOL-5-YL]ACETIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:114 , THR B:391 , THR B:409 , ASN B:411 , GLN B:430 , ASP B:433 , TYR B:444 , SER B:462 , SER B:463 , MET B:464 , GLY B:484 , HOH B:611 , HOH B:692BINDING SITE FOR RESIDUE AVN B 390
2AC2SOFTWAREARG C:114 , THR D:391 , THR D:409 , ASN D:411 , GLN D:430 , ASP D:433 , TYR D:444 , SER D:462 , SER D:463 , MET D:464 , GLY D:484 , HOH D:628 , HOH D:684BINDING SITE FOR RESIDUE AVN D 390

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z8K)

(-) 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 2Z8K)

(-) 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 2Z8K)

(-) 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:350
 aligned with GGT_ECOLI | P18956 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:350
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387
            GGT_ECOLI    38 EDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 2z8k A  38 EDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387


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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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........eeee.....eeee........eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE G_GLU_TRANSPEPTIDASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z8k B 391 TTHYSVVDKDGNAVAVTYTLNTTFGTGIVAGESGILLNNQMDDFSAKPGVPNVYGLVGGDANAVGPNKRPLSSMSPTIVVKDGKTWLVTGSPGGSRIITTVLQMVVNSIDYGLNVAEATNAPRFHHQWLPDELRVEKGFSPDTLKLLEAKGQKVALKEAMGSTQSIMVGPDGELYGASDPRSVDDLTAGY 580
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580


Chain C from PDB  Type:PROTEIN  Length:350
 aligned with GGT_ECOLI | P18956 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:350
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387
            GGT_ECOLI    38 EDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 2z8k C  38 EDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387


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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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........eeee.....eeee........eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE G_GLU_TRANSPEPTIDASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z8k D 391 TTHYSVVDKDGNAVAVTYTLNTTFGTGIVAGESGILLNNQMDDFSAKPGVPNVYGLVGGDANAVGPNKRPLSSMSPTIVVKDGKTWLVTGSPGGSRIITTVLQMVVNSIDYGLNVAEATNAPRFHHQWLPDELRVEKGFSPDTLKLLEAKGQKVALKEAMGSTQSIMVGPDGELYGASDPRSVDDLTAGY 580
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580
   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  (0, 0)

(no "SCOP Domain" information available for 2Z8K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z8K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z8K)

(-) 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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  2.3.2.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        GGT_ECOLI | P18956: 2dbu 2dbw 2dbx 2dg5 2e0w 2e0x 2e0y 2z8i 2z8j 5b5t

(-) Related Entries Specified in the PDB File

2z8i THE SAMA PROTEIN IN COMPLEX WITH AZASERINE
2z8j THE SAME PROTEIN IN COMPLEX WITH AZASERINE WITH A DIAZO- GROUP