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Title :   STRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST CU,ZN ENZYME SUPEROXIDE DISMUTASE

Authors :   K. Djinovic, G. Gatti, A. Coda, L. Antolini, G. Pelosi, A. Desideri, M. Falconi, F. Marmocchi, G. Rotilio, M. Bolognesi

Date :   14 Jun 91 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Oxidoreductase(Superoxide Acceptor) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Djinovic, G. Gatti, A. Coda, L. Antolini, G. Pelosi, A. Desideri, M. Falconi, F. Marmocchi, G. Rolilio, M. Bolognesi
Structure Solution And Molecular Dynamics Refinement Of The Yeast Cu, Zn Enzyme Superoxide Dismutase.
Acta Crystallogr. , Sect. B V. 47 918 1991
PubMed-ID: 1772629 | Reference-DOI: 10.1107/S0108768191004949
(for further references see the PDB file header)

Molecule 1 - COPPER,ZINC SUPEROXIDE DISMUTASE
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	A	UNKNOWN	HIS A:44 , HIS A:46 , HIS A:61 , HIS A:118 , HIS A:69 , HIS A:78 , ASP A:81 , CU A:152 , ZN A:153	NULL
02	AC1	SOFTWARE	HIS A:44 , HIS A:46 , HIS A:61 , HIS A:118 , HOH A:154	BINDING SITE FOR RESIDUE CU A 152
03	AC2	SOFTWARE	HIS A:61 , HIS A:69 , HIS A:78 , ASP A:81	BINDING SITE FOR RESIDUE ZN A 153
04	AC3	SOFTWARE	HIS B:44 , HIS B:46 , HIS B:61 , HIS B:118 , HOH B:154	BINDING SITE FOR RESIDUE CU B 152
05	AC4	SOFTWARE	HIS B:61 , HIS B:69 , HIS B:78 , ASP B:81	BINDING SITE FOR RESIDUE ZN B 153
06	AC5	SOFTWARE	HIS C:44 , HIS C:46 , HIS C:61 , HIS C:118 , HOH C:154	BINDING SITE FOR RESIDUE CU C 152
07	AC6	SOFTWARE	HIS C:61 , HIS C:69 , HIS C:78 , ASP C:81	BINDING SITE FOR RESIDUE ZN C 153
08	AC7	SOFTWARE	HIS D:44 , HIS D:46 , HIS D:61 , HIS D:118 , HOH D:154	BINDING SITE FOR RESIDUE CU D 152
09	AC8	SOFTWARE	HIS D:61 , HIS D:69 , HIS D:78 , ASP D:81	BINDING SITE FOR RESIDUE ZN D 153
10	B	UNKNOWN	HIS B:44 , HIS B:46 , HIS B:61 , HIS B:118 , HIS B:69 , HIS B:78 , ASP B:81 , CU B:152 , ZN B:153	NULL
11	C	UNKNOWN	HIS C:44 , HIS C:46 , HIS C:61 , HIS C:118 , HIS C:69 , HIS C:78 , ASP C:81 , CU C:152 , ZN C:153	NULL
12	D	UNKNOWN	HIS D:44 , HIS D:46 , HIS D:61 , HIS D:118 , HIS D:69 , HIS D:78 , ASP D:81 , CU D:152 , ZN D:153	NULL

Asymmetric/Biological Unit

No.	Residues
1	A:55	-	A:144
2	B:55	-	B:144
3	C:55	-	C:144
4	D:55	-	D:144

(no "Cis Peptide Bond" information available for 1SDY)

(no "SAP(SNP)/Variant" information available for 1SDY)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_1	PS00087	Copper/Zinc superoxide dismutase signature 1.	SODC_YEAST	45-55	4	A:42-52 B:42-52 C:42-52 D:42-52
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_YEAST	139-150	4	A:136-147 B:136-147 C:136-147 D:136-147

Asymmetric/Biological Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YJR104C	1	YJR104C.1	X:623002-622538	465	SODC_YEAST	1-154	154	4	A:2-151 B:2-151 C:2-151 D:2-151	153 153 153 153

Asymmetric/Biological Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:153
 aligned with SODC_YEAST | P00445 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           SODC_YEAST     2 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 154
               SCOP domains d1sdya_ A: Cu,Zn superoxide dismutase, SOD                                                                                                                SCOP domains
               CATH domains 1sdyA00 A:2-151  [code=2.60.40.200, no name defined]                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.......eeeeeeeee.....eeeeeee..................................eeeeee......eeeeeee..............eeee............hhhhhh.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ---- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-151 UniProt: 1-154 [INCOMPLETE]                                                                                                        Transcript 1
                 1sdy A   2 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 151
                                    11        21    ||  29      | 38        48        58        68        78        88        98       108       118       128       138       148   
                                                  25A|        35A                                                                                                                    
                                                   25B

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with SODC_YEAST | P00445 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           SODC_YEAST     2 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 154
               SCOP domains d1sdyb_ B: Cu,Zn superoxide dismutase, SOD                                                                                                                SCOP domains
               CATH domains 1sdyB00 B:2-151  [code=2.60.40.200, no name defined]                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.......eeeeeeeee.....eeeeeee..................................eeeeee......eeeeeee..............eeee............hhhhhh.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ---- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-151 UniProt: 1-154 [INCOMPLETE]                                                                                                        Transcript 1
                 1sdy B   2 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 151
                                    11        21    ||  29      | 38        48        58        68        78        88        98       108       118       128       138       148   
                                                  25A|        35A                                                                                                                    
                                                   25B

Chain C from PDB  Type:PROTEIN  Length:153
 aligned with SODC_YEAST | P00445 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           SODC_YEAST     2 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 154
               SCOP domains d1sdyc_ C: Cu,Zn superoxide dismutase, SOD                                                                                                                SCOP domains
               CATH domains 1sdyC00 C:2-151  [code=2.60.40.200, no name defined]                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.......eeeeeeeee.....eeeeeee..................................eeeeee......eeeeeee..............eeee............hhhhhh.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ---- PROSITE
               Transcript 1 Exon 1.1  PDB: C:2-151 UniProt: 1-154 [INCOMPLETE]                                                                                                        Transcript 1
                 1sdy C   2 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 151
                                    11        21    ||  29      | 38        48        58        68        78        88        98       108       118       128       138       148   
                                                  25A|        35A                                                                                                                    
                                                   25B

Chain D from PDB  Type:PROTEIN  Length:153
 aligned with SODC_YEAST | P00445 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           SODC_YEAST     2 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 154
               SCOP domains d1sdyd_ D: Cu,Zn superoxide dismutase, SOD                                                                                                                SCOP domains
               CATH domains 1sdyD00 D:2-151  [code=2.60.40.200, no name defined]                                                                                                      CATH domains
           Pfam domains (1) --Sod_Cu-1sdyD01 D:4-147                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) --Sod_Cu-1sdyD02 D:4-147                                                                                                                             ---- Pfam domains (2)
           Pfam domains (3) --Sod_Cu-1sdyD03 D:4-147                                                                                                                             ---- Pfam domains (3)
           Pfam domains (4) --Sod_Cu-1sdyD04 D:4-147                                                                                                                             ---- Pfam domains (4)
         Sec.struct. author .eeeeee......eeeeeee.......eeeeeeeee.....eeeeeee..................................eeeeee......eeeeeee..............eeee............hhhhhh.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ---- PROSITE
               Transcript 1 Exon 1.1  PDB: D:2-151 UniProt: 1-154 [INCOMPLETE]                                                                                                        Transcript 1
                 1sdy D   2 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 151
                                    11        21    ||  29      | 38        48        58        68        78        88        98       108       118       128       138       148   
                                                  25A|        35A                                                                                                                    
                                                   25B

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Cu,Zn superoxide dismutase-like (165)

Family: Cu,Zn superoxide dismutase-like (158)

Protein domain: Cu,Zn superoxide dismutase, SOD (134)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (12)

1a	d1sdya_	A:
1b	d1sdyb_	B:
1c	d1sdyc_	C:
1d	d1sdyd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.200, no name defined] (125)

Baker's yeast (Saccharomyces cerevisiae) (13)

1a	1sdyA00	A:2-151
1b	1sdyB00	B:2-151
1c	1sdyC00	C:2-151
1d	1sdyD00	D:2-151

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Sod_Cu] (71)

Family: Sod_Cu (71)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (5)

1a	Sod_Cu-1sdyD01	D:4-147
1b	Sod_Cu-1sdyD02	D:4-147
1c	Sod_Cu-1sdyD03	D:4-147
1d	Sod_Cu-1sdyD04	D:4-147

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (SODC_YEAST | P00445)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0001320	age-dependent response to reactive oxygen species involved in chronological cell aging	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.) occurring in non-dividing cells as they age as a result of reactive oxygen species, where the change varies according to the age of the cell or organism.
	GO:0006878	cellular copper ion homeostasis	Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0006882	cellular zinc ion homeostasis	Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell.
	GO:0031505	fungal-type cell wall organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fungal-type cell wall.
	GO:1901856	negative regulation of cellular respiration	Any process that stops, prevents or reduces the frequency, rate or extent of cellular respiration.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0051091	positive regulation of sequence-specific DNA binding transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0036091	positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress	Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0050821	protein stabilization	Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
	GO:0019430	removal of superoxide radicals	Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
	GO:0006801	superoxide metabolic process	The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	1sdy
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Description

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Ligands, Modified Residues, Ions (2, 8)

Sites (12, 12)

SS Bonds (4, 4)

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Exons (1, 4)

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