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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI GAMMA-GLUTAMYLTRANSPEPTIDASE IN COMPLEX WITH PEPTIDYL PHOSPHONATE INHIBITOR 1B
 
Authors :  K. Wada, K. Fukuyama
Date :  18 May 16  (Deposition) - 28 Sep 16  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Glutathione, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kamiyama, M. Nakajima, L. Han, K. Wada, M. Mizutani, Y. Tabuchi, A. Kojima-Yuasa, I. Matsui-Yuasa, H. Suzuki, K. Fukuyama, B. Watanabe, J. Hiratake
Phosphonate-Based Irreversible Inhibitors Of Human Gamma-Glutamyl Transpeptidase (Ggt). Ggstop Is A Non-Toxic And Highly Selective Inhibitor With Critical Electrostatic Interaction With An Active-Site Residue Lys562 For Enhanced Inhibitory Activity
Bioorg. Med. Chem. V. 24 5340 2016
PubMed-ID: 27622749  |  Reference-DOI: 10.1016/J.BMC.2016.08.050

(-) Compounds

Molecule 1 - GAMMA-GLUTAMYLTRANSPEPTIDASE LARGE CHAIN
    Chains: A, C
    EC Number: 2.3.2.2, 3.4.19.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GGT, B3447, JW3412
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: GLUTATHIONE HYDROLASE, GAMMA-GLUTAMYLTRANSPEPTIDASE LARGE- SUBUNIT
 
Molecule 2 - GAMMA-GLUTAMYLTRANSPEPTIDASE SMALL CHAIN
    Chains: B, D
    EC Number: 2.3.2.2, 3.4.19.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GGT, B3447, JW3412
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: GLUTATHIONE HYDROLASE, GAMMA-GLUTAMYLTRANSPEPTIDASE SMALL- SUBUNIT

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
16FY2Ligand/Ion(2~{S})-2-AZANYL-4-[(2~{R})-1-(2-HYDROXY-2-OXOETHYLAMINO)-1-OXIDANYLIDENE-BUTAN-2-YL]OXYPHOSPHONOYL-BUTANOIC ACID
2CA2Ligand/IonCALCIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16FY1Ligand/Ion(2~{S})-2-AZANYL-4-[(2~{R})-1-(2-HYDROXY-2-OXOETHYLAMINO)-1-OXIDANYLIDENE-BUTAN-2-YL]OXYPHOSPHONOYL-BUTANOIC ACID
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16FY1Ligand/Ion(2~{S})-2-AZANYL-4-[(2~{R})-1-(2-HYDROXY-2-OXOETHYLAMINO)-1-OXIDANYLIDENE-BUTAN-2-YL]OXYPHOSPHONOYL-BUTANOIC ACID
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:114 , THR B:391 , ASN B:411 , GLN B:430 , ASP B:433 , TYR B:444 , SER B:462 , SER B:463 , MET B:464 , PRO B:482 , GLY B:483 , GLY B:484 , ILE B:487 , GLY B:551 , HOH B:732 , HOH B:805binding site for residue 6FY B 600
2AC2SOFTWAREASP B:569 , SER B:572 , ASP B:575 , HOH B:768 , HOH B:836 , HOH B:839 , HOH B:843binding site for residue CA B 601
3AC3SOFTWAREASP D:569 , SER D:572 , ASP D:575 , HOH D:769 , HOH D:803 , HOH D:837 , HOH D:840binding site for residue CA D 601
4AC4SOFTWAREALA C:90 , ARG C:114 , HOH C:603 , THR D:392 , THR D:407 , TYR D:408 , THR D:409 , ASN D:411 , THR D:412 , THR D:413 , GLN D:430 , ASP D:433 , TYR D:444 , SER D:462 , SER D:463 , MET D:464 , PRO D:482 , GLY D:483 , GLY D:484 , ILE D:487 , GLY D:551 , HOH D:720 , HOH D:762 , HOH D:810 , HOH D:822binding site for Di-peptide 6FY D 600 and THR D 391

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B5T)

(-) 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 5B5T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B5T)

(-) Exons   (0, 0)

(no "Exon" information available for 5B5T)

(-) 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               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
                 5b5t A  39 DVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
                                    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         


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               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.......eeeee.....eeeee.......eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b5t 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               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.....hhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b5t C  39 DVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYE 387
                                    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         


Chain D from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               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.......eeeee.....eeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b5t 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 5B5T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B5T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B5T)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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        GGT_ECOLI | P18956: 2dbu 2dbw 2dbx 2dg5 2e0w 2e0x 2e0y 2z8i 2z8j 2z8k

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