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(-) Description

Title :  ACYL-ENZYME INTERMEDIATE BETWEEN ALR0975 AND GLUTATHIONE AT PH 3.4
 
Authors :  D. Vivares, P. Arnoux, D. Pignol
Date :  08 Jun 05  (Deposition) - 14 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Phytochelatin Synthase, Pcs, Alr0975, Acyl-Enzyme Intermediate, Nostoc, Glutathione Metabolism, Cysteine Protease, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Vivares, P. Arnoux, D. Pignol
A Papain-Like Enzyme At Work: Native And Acyl- Enzyme Intermediate Structures In Phytochelatin Synthesis.
Proc. Natl. Acad. Sci. Usa V. 102 18848 2005
PubMed-ID: 16339904  |  Reference-DOI: 10.1073/PNAS.0505833102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALR0975 PROTEIN
    Chains: A, B
    EC Number: 2.3.2.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJC40
    Expression System Taxid: 562
    Organism Common: NOSTOC SP. PCC 7120
    Organism Scientific: ANABAENA SP.
    Organism Taxid: 1167
    Synonym: PRIMITIVE PHYTOCHELATIN SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
13GC2Ligand/IonGAMMA-GLUTAMYLCYSTEINE
2CA2Ligand/IonCALCIUM ION
3CL2Ligand/IonCHLORIDE ION
4MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
13GC1Ligand/IonGAMMA-GLUTAMYLCYSTEINE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
13GC1Ligand/IonGAMMA-GLUTAMYLCYSTEINE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:100BINDING SITE FOR RESIDUE CL A1241
2AC2SOFTWAREASP A:53 , ASN A:159 , GLN A:162 , ASN A:165BINDING SITE FOR RESIDUE CA A1242
3AC3SOFTWAREGLN B:100 , HOH B:2046BINDING SITE FOR RESIDUE CL B1241
4AC4SOFTWAREASP B:53 , ASN B:159 , GLN B:162 , ASN B:165BINDING SITE FOR RESIDUE CA B1242
5AC5SOFTWAREGLN A:64 , GLN A:67 , ALA A:68 , TYR A:69 , CYS A:70 , GLY A:122 , MSE A:123 , ASN A:170 , GLY A:182 , ILE A:184 , ASP A:225 , ARG A:232 , HOH A:2043 , HOH A:2083 , HOH A:2085 , HOH A:2174BINDING SITE FOR RESIDUE 3GC A1240
6AC6SOFTWAREGLN B:64 , GLN B:67 , ALA B:68 , TYR B:69 , CYS B:70 , GLY B:122 , MSE B:123 , ASN B:170 , GLY B:182 , ASP B:225 , ARG B:232 , HOH B:2061 , HOH B:2204 , HOH B:2205BINDING SITE FOR RESIDUE 3GC B1240

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BU3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:93 -Pro B:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BU3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BU3)

(-) Exons   (0, 0)

(no "Exon" information available for 2BU3)

(-) 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:200
 aligned with Q8YY76_NOSS1 | Q8YY76 from UniProtKB/TrEMBL  Length:242

    Alignment length:211
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238 
         Q8YY76_NOSS1    29 LSPNLIGFNSNEGEKLLLTSRSREDFFPLSMQFVTQVNQAYCGVASIIMVLNSLGINAPETAQYSPYRVFTQDNFFSNEKTKAVIAPEVVARQGMTLDELGRLIASYGVKVKVNHASDTNIEDFRKQVAENLKQDGNFVIVNYLRKEIGQERGGHISPLAAYNEQTDRFLIMDVSRYKYPPVWVKTTDLWKAMNTVDSVSQKTRGFVFVSK 239
               SCOP domains d2bu3a_ A: Primitive phytochelatin synthase                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..hhhhhhhhhhh....hhhhhhhhh.......hhhhhhhhhhhhhh....--------...........---.....hhhhhhhhh.hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh...eeeeeeee.hhhh....eeeeeeeeee....eeee..........eeeehhhhhhhhh.ee....ee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bu3 A  29 LSPNLIGFNSNEGEKLLLTSRSREDFFPLSmQFVTQVNQAYCGVASIImVLNSLGINA--------YRVFTQDNFFS---TKAVIAPEVVARQGmTLDELGRLIASYGVKVKVNHASDTNIEDFRKQVAENLKQDGNFVIVNYLRKEIGQERGGHISPLAAYNEQTDRFLImDVSRYKYPPVWVKTTDLWKAmNTVDSVSQKTRGFVFVSK 239
                                    38        48        58|       68        78       | -      | 98      |  -|      118    |  128       138       148       158       168       178       188       198 |     208       218  |    228       238 
                                                         59-MSE            77-MSE   86       95       105 109           123-MSE                                                                      200-MSE              221-MSE              


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with Q8YY76_NOSS1 | Q8YY76 from UniProtKB/TrEMBL  Length:242

    Alignment length:208
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
         Q8YY76_NOSS1    32 NLIGFNSNEGEKLLLTSRSREDFFPLSMQFVTQVNQAYCGVASIIMVLNSLGINAPETAQYSPYRVFTQDNFFSNEKTKAVIAPEVVARQGMTLDELGRLIASYGVKVKVNHASDTNIEDFRKQVAENLKQDGNFVIVNYLRKEIGQERGGHISPLAAYNEQTDRFLIMDVSRYKYPPVWVKTTDLWKAMNTVDSVSQKTRGFVFVSK 239
               SCOP domains d2bu3b_ B: Primitive phytochelatin synthase                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhhhhhh.....hhhhhhhhh.......hhhhhhhhhhhhhhh....----..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....eeeeeeee.hhhh....eeeeeeeeee....eeee..........eeeehhhhhhhhh.ee....ee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bu3 B  32 NLIGFNSNEGEKLLLTSRSREDFFPLSmQFVTQVNQAYCGVASIImVLNSLGINAP----YSPYRVFTQDNFFSNEKTKAVIAPEVVARQGmTLDELGRLIASYGVKVKVNHASDTNIEDFRKQVAENLKQDGNFVIVNYLRKEIGQERGGHISPLAAYNEQTDRFLImDVSRYKYPPVWVKTTDLWKAmNTVDSVSQKTRGFVFVSK 239
                                    41        51       |61        71     |  81     |   -|      101       111       121 |     131       141       151       161       171       181       191       201       211       221       231        
                                                      59-MSE            77-MSE    87   92                            123-MSE                                                                      200-MSE              221-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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BU3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BU3)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8YY76_NOSS1 | Q8YY76)
molecular function
    GO:0016756    glutathione gamma-glutamylcysteinyltransferase activity    Catalysis of the reaction: glutathione + Glu(-Cys)(n)-Gly = Gly + Glu(-Cys)(n+1)-Gly.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0046938    phytochelatin biosynthetic process    The chemical reactions and pathways resulting in the formation of phytochelatins, any of a group of peptides that bind metals (Cd, Zn, Cu, Pb, Hg) in thiolate coordination complexes. The structure is of the type (gamma-glutamyl-cysteinyl)n-glycine, where n is 2 to 11.
    GO:0010038    response to metal ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8YY76_NOSS1 | Q8YY76: 2btw

(-) Related Entries Specified in the PDB File

2btw CRYSTAL STRUCTURE OF ALR0975