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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GAMMA-GLUTAMYLTRANSPEPTIDASE IN COMPLEX WITH GLUTAMATE
 
Authors :  J. J. Barycki, A. Sand, G. Boanca
Date :  14 Jul 07  (Deposition) - 12 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Ntn-Hydrolase, Glutamyltranspeptidase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Morrow, K. Williams, A. Sand, G. Boanca, J. J. Barycki
Characterization Of Helicobacter Pylori Gamma-Glutamyltranspeptidase Reveals The Molecular Basis Fo Substrate Specificity And A Critical Role For The Tyrosine 433-Containing Loop In Catalysis.
Biochemistry V. 46 13407 2007
PubMed-ID: 17960917  |  Reference-DOI: 10.1021/BI701599E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAMMA-GLUTAMYLTRANSPEPTIDASE
    Chains: A, C
    EC Number: 2.3.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 25-379
    Gene: HP_1118
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Synonym: GGT
 
Molecule 2 - GAMMA-GLUTAMYLTRANSPEPTIDASE
    Chains: B, D
    EC Number: 2.3.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 380-567
    Gene: HP_1118
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Synonym: GGT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GLU2Mod. Amino AcidGLUTAMIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GLU2Mod. Amino AcidGLUTAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GLU1Mod. Amino AcidGLUTAMIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GLU1Mod. Amino AcidGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:103 , THR B:380 , ASN B:400 , GLU B:419 , ASP B:422 , TYR B:433 , SER B:451 , SER B:452 , MET B:453 , GLY B:472 , GLY B:473 , ILE B:476 , HOH B:608 , HOH B:692BINDING SITE FOR RESIDUE GLU B 1
2AC2SOFTWAREARG C:103 , THR D:380 , ASN D:400 , GLU D:419 , ASP D:422 , TYR D:433 , SER D:451 , SER D:452 , MET D:453 , GLY D:472 , GLY D:473 , ILE D:476 , HOH D:580BINDING SITE FOR RESIDUE GLU D 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QM6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:281 -Pro A:282
2Leu B:508 -Pro B:509
3Pro C:281 -Pro C:282
4Leu D:508 -Pro D:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QM6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QM6)

(-) Exons   (0, 0)

(no "Exon" information available for 2QM6)

(-) 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:342
 aligned with O25743_HELPY | O25743 from UniProtKB/TrEMBL  Length:567

    Alignment length:342
                                    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  
         O25743_HELPY    32 IKNTKVGLALSSHPLASEIGQKVLEEGGNAIDAAVAIGFALAVVHPAAGNIGGGGFAVIHLANGENVALDFREKAPLKATKNMFLDKQGNVVPKLSEDGYLAAGVPGTVAGMEAMLKKYGTKKLSQLIDPAIKLAENGYAISQRQAETLKEARERFLKYSSSKKYFFKKGHLDYQEGDLFVQKDLAKTLNQIKTLGAKGFYQGQVAELIEKDMKKNGGIITKEDLASYNVKWRKPVVGSYRGYKIISMSPPSSGGTHLIQILNVMENADLSALGYGASKNIHIAAEAMRQAYADRSVYMGDADFVSVPVDKLINKAYAKKIFDTIQPDTVTPSSQIKPGMGQ 373
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...eeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeeee.....eeeeee...........................hhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhh.hhhhhhhhee...ee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh..eee..eeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qm6 A  32 IKNTKVGLALSSHPLASEIGQKVLEEGGNAIDAAVAIGFALAVVHPAAGNIGGGGFAVIHLANGENVALDFREKAPLKATKNMFLDKQGNVVPKLSEDGYLAAGVPGTVAGMEAMLKKYGTKKLSQLIDPAIKLAENGYAISQRQAETLKEARERFLKYSSSKKYFFKKGHLDYQEGDLFVQKDLAKTLNQIKTLGAKGFYQGQVAELIEKDMKKNGGIITKEDLASYNVKWRKPVVGSYRGYKIISMSPPSSGGTHLIQILNVMENADLSALGYGASKNIHIAAEAMRQAYADRSVYMGDADFVSVPVDKLINKAYAKKIFDTIQPDTVTPSSQIKPGMGQ 373
                                    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  


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with O25743_HELPY | O25743 from UniProtKB/TrEMBL  Length:567

    Alignment length:187
                                   389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       
         O25743_HELPY   380 TTHYSVADRWGNAVSVTYTINASYGSAASIDGAGFLLNNEMDDFSIKPGNPNLYGLVGGDANAIEANKRPLSSMSPTIVLKNNKVFLVVGSPGGSRIITTVLQVISNVIDYNMNISEAVSAPRFHMQWLPDELRIEKFGMPADVKDNLTKMGYQIVTKPVMGDVNAIQVLPKTKGSVFYGSTDPRKE 566
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee...................hhhhhh................................eeeee..eeeeee...hhhhhhhhhhhhhhhhhh...hhhhhhhh...........eee.....hhhhhhhhhhhh..eee........eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qm6 B 380 TTHYSVADRWGNAVSVTYTINASYGSAASIDGAGFLLNNEMDDFSIKPGNPNLYGLVGGDANAIEANKRPLSSMSPTIVLKNNKVFLVVGSPGGSRIITTVLQVISNVIDYNMNISEAVSAPRFHMQWLPDELRIEKFGMPADVKDNLTKMGYQIVTKPVMGDVNAIQVLPKTKGSVFYGSTDPRKE   1
                                   389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559     ||
                                                                                                                                                                                                                   565|
                                                                                                                                                                                                                      1


Chain C from PDB  Type:PROTEIN  Length:348
 aligned with O25743_HELPY | O25743 from UniProtKB/TrEMBL  Length:567

    Alignment length:348
                                    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        
         O25743_HELPY    32 IKNTKVGLALSSHPLASEIGQKVLEEGGNAIDAAVAIGFALAVVHPAAGNIGGGGFAVIHLANGENVALDFREKAPLKATKNMFLDKQGNVVPKLSEDGYLAAGVPGTVAGMEAMLKKYGTKKLSQLIDPAIKLAENGYAISQRQAETLKEARERFLKYSSSKKYFFKKGHLDYQEGDLFVQKDLAKTLNQIKTLGAKGFYQGQVAELIEKDMKKNGGIITKEDLASYNVKWRKPVVGSYRGYKIISMSPPSSGGTHLIQILNVMENADLSALGYGASKNIHIAAEAMRQAYADRSVYMGDADFVSVPVDKLINKAYAKKIFDTIQPDTVTPSSQIKPGMGQLHEGSN 379
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...eeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeeee.....eeeeee...........................hhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh..eee..eeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh......hhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qm6 C  32 IKNTKVGLALSSHPLASEIGQKVLEEGGNAIDAAVAIGFALAVVHPAAGNIGGGGFAVIHLANGENVALDFREKAPLKATKNMFLDKQGNVVPKLSEDGYLAAGVPGTVAGMEAMLKKYGTKKLSQLIDPAIKLAENGYAISQRQAETLKEARERFLKYSSSKKYFFKKGHLDYQEGDLFVQKDLAKTLNQIKTLGAKGFYQGQVAELIEKDMKKNGGIITKEDLASYNVKWRKPVVGSYRGYKIISMSPPSSGGTHLIQILNVMENADLSALGYGASKNIHIAAEAMRQAYADRSVYMGDADFVSVPVDKLINKAYAKKIFDTIQPDTVTPSSQIKPGMGQLHEGSN 379
                                    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        


Chain D from PDB  Type:PROTEIN  Length:187
 aligned with O25743_HELPY | O25743 from UniProtKB/TrEMBL  Length:567

    Alignment length:187
                                   389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       
         O25743_HELPY   380 TTHYSVADRWGNAVSVTYTINASYGSAASIDGAGFLLNNEMDDFSIKPGNPNLYGLVGGDANAIEANKRPLSSMSPTIVLKNNKVFLVVGSPGGSRIITTVLQVISNVIDYNMNISEAVSAPRFHMQWLPDELRIEKFGMPADVKDNLTKMGYQIVTKPVMGDVNAIQVLPKTKGSVFYGSTDPRKE 566
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) G_glu_transpept-2qm6D01 D:380-1                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) G_glu_transpept-2qm6D02 D:380-1                                                                                                                                                             Pfam domains (2)
           Pfam domains (3) G_glu_transpept-2qm6D03 D:380-1                                                                                                                                                             Pfam domains (3)
           Pfam domains (4) G_glu_transpept-2qm6D04 D:380-1                                                                                                                                                             Pfam domains (4)
         Sec.struct. author .eeeeeee....eeeeeee...................hhhhhh................................eeeee..eeeeee...hhhhhhhhhhhhhhhhhh...hhhhhhhh...........eee.....hhhhhhhhhhhh..eee........eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qm6 D 380 TTHYSVADRWGNAVSVTYTINASYGSAASIDGAGFLLNNEMDDFSIKPGNPNLYGLVGGDANAIEANKRPLSSMSPTIVLKNNKVFLVVGSPGGSRIITTVLQVISNVIDYNMNISEAVSAPRFHMQWLPDELRIEKFGMPADVKDNLTKMGYQIVTKPVMGDVNAIQVLPKTKGSVFYGSTDPRKE   1
                                   389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559     ||
                                                                                                                                                                                                                   565|
                                                                                                                                                                                                                      1
   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 2QM6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QM6)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NTN (93)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O25743_HELPY | O25743)
molecular function
    GO:0003840    obsolete gamma-glutamyltransferase activity    OBSOLETE. Catalysis of the reaction: (5-L-glutamyl)-peptide + an amino acid = peptide + 5-L-glutamyl-amino acid.
biological process
    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:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:1902807    negative regulation of cell cycle G1/S phase transition    Any process that stops, prevents or reduces the frequency, rate or extent of cell cycle G1/S phase transition.
    GO:0032757    positive regulation of interleukin-8 production    Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.

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  2qm6
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  O25743_HELPY | O25743
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  2.3.2.2
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 Related Entries

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

UniProtKB/TrEMBL
        O25743_HELPY | O25743: 2nqo 2qmc 3fnm 5bpk

(-) Related Entries Specified in the PDB File

2nqo APOENZYME
2qmc