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(-) Description

Title :  COPPER-ZINC SUPEROXIDE DISMUTASE IS ACTIVATED THROUGH A SULFENIC ACID INTERMEDIATE AT A COPPER-ION ENTRY SITE
 
Authors :  A. B. Taylor, P. J. Hart, D. D. Winkler
Date :  16 Dec 16  (Deposition) - 31 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Oxidoreductase-Chaperone Complex, Cu-Zn Superoxide Dismutase, Metallochaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Fetherolf, S. D. Boyd, A. B. Taylor, H. J. Kim, J. A. Wohlschlegel, N. J. Blackburn, P. J. Hart, D. R. Winge, D. D. Winkler
Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate At A Copper-Ion Entry Site.
J. Biol. Chem. 2017
PubMed-ID: 28533431  |  Reference-DOI: 10.1074/JBC.M117.775981

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [CU-ZN]
    Chains: A, C
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Plasmid: YEP351
    Expression System Strain: EG118
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Gene: SOD1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SUPEROXIDE DISMUTASE 1,HSOD1
 
Molecule 2 - SUPEROXIDE DISMUTASE 1 COPPER CHAPERONE
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PKA6H
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CCS1, LYS7, YMR038C, YM9532.03C
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 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, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:63 , HIS A:71 , HIS A:80 , ASP A:83binding site for residue ZN A 201
2AC2SOFTWARECYS B:17 , CYS B:20 , CYS D:17 , CYS D:20binding site for residue ZN B 301
3AC3SOFTWAREHIS C:63 , HIS C:71 , HIS C:80 , ASP C:83binding site for residue ZN C 201

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1D:27 -D:64

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5U9M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U9M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U9M)

(-) Exons   (0, 0)

(no "Exon" information available for 5U9M)

(-) 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:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee.......eeeeeeee....eeeeeee........hhhhhh.....................eeeeeee.....eeeeeee.....hhhhh....eeeee............hhhhhh....eeeeee.eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u9m A   1 ATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFRVQEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhh....eeeeeee....eeeeee..hhhhhhhhh..eee.......eeeeeeee.............eeeeeeeee.....eeeeeeeeee...eeeeeeee......hhhhhhh.eeeeeeeeeee.ee.......eeeeeeeee..hhhhh...eeeeeee............eeeeeee.ee.........eee.....eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u9m B   8 EATYAICENCVNDIKACLKNVPGINSLNFDIEQQIMSVESSVAPSTIINTLDAIIRGAGKPNSSAVAILETFQKYTIDQKKDTAVRGLARIVQVGENKTLFDITVNGVPEAGNYHASIHEKGDVSKGVESTGKVWHKFDEPIECFNESDLGKNLYSGKTFLSAPLPTWQLIGRSFVISKSLNHPENEPSSVKDYSFLGVIARSAGVWENNKQVCACTGKTVWAAAK 241
                                 || 20        30        40        50        60||      75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235      
                                13|                                          61|                                                                                                                                                                              
                                 17                                           67                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee.......eeeeeeee....eeeeeee........hhhhhh.....................eeeeeee.....eeeeeee.....hhhhh....eeeee..........hhhhhhhh....eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u9m C   1 ATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFRVQEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   


Chain D from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhh....eeeeeee....eeeeee..hhhhhhhhhhh.....eee.......eeeeeeee.............eeeeeeeee.....eeeeeeeeee...eeeeeeee......hhhhhhh.eeeeeeeeeee.eee..eeeeeeeeeeeee..hhhhh...eeeeeee..hhhhh.....eeeeeee.eee........eee.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u9m D   6 TYEATYAIPCENCVNDIKACLKNVPGINSLNFDIEQQIMSVESSVAPSTIINTLRNCGKDAIIRGAGKPNSSAVAILETFQKYTIDQKKDTAVRGLARIVQVGENKTLFDITVNGVPEAGNYHASIHEKGDVSKGVESTGKVWHKFDEPIECFNESDLGKNLYSGKTFLSAPLPTWQLIGRSFVISKSLNHPENEPSSVKDYSFLGVIARSAGVWENNKQVCACTGKTVWAAAK 241
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237    
                                   14|                                                                                                                                                                                                                                
                                    17
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  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 5U9M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U9M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U9M)

(-) Gene Ontology  (105, 118)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        CCS1_YEAST | P40202: 1ej8 1jk9 1qup
        SODC_HUMAN | P00441: 1azv 1ba9 1dsw 1fun 1hl4 1hl5 1kmg 1l3n 1mfm 1n18 1n19 1oez 1ozt 1ozu 1p1v 1ptz 1pu0 1rk7 1sos 1spd 1uxl 1uxm 2af2 2c9s 2c9u 2c9v 2gbt 2gbu 2gbv 2lu5 2mp3 2nam 2nnx 2r27 2v0a 2vr6 2vr7 2vr8 2wko 2wyt 2wyz 2wz0 2wz5 2wz6 2xjk 2xjl 2zkw 2zkx 2zky 3cqp 3cqq 3ecu 3ecv 3ecw 3gqf 3gtv 3gzo 3gzp 3gzq 3h2p 3h2q 3hff 3k91 3kh3 3kh4 3ltv 3qqd 3re0 3t5w 4a7g 4a7q 4a7s 4a7t 4a7u 4a7v 4b3e 4bcy 4bcz 4bd4 4ff9 4mcm 4mcn 4nin 4nio 4nip 4oh2 4sod 4xcr 5dli 5iiw 5j07 5j0c 5j0f 5j0g 5k02

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