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Title :   STRUCTURE OF THE CYTOSOLIC CU,ZN SOD FROM S. MANSONI

Authors :   R. M. F. Cardoso, C. H. T. P. Silva, A. P. Ulian De Araujo, T. Tanaka, M. Tanaka, R. C. Garratt

Date :   12 Jun 04 (Deposition) - 31 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x)

Keywords :   Beta-Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. M. Cardoso, C. H. Silva, A. P. Ulian De Araujo, T. Tanaka, M. Tanaka, R. C. Garratt
Structure Of The Cytosolic Cu, Zn Superoxide Dismutase From Schistosoma Mansoni.
Acta Crystallogr. , Sect. D V. 60 1569 2004
PubMed-ID: 15333927 | Reference-DOI: 10.1107/S0907444904016798
(for further references see the PDB file header)

Molecule 1 - SUPEROXIDE DISMUTASE
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-4T-1
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	SOD
	Organism Scientific	:	SCHISTOSOMA MANSONI
	Organism Taxid	:	6183

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

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

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:62 , HIS A:70 , HIS A:79 , ASP A:82	BINDING SITE FOR RESIDUE ZN A 711
2	AC2	SOFTWARE	HIS A:45 , HIS A:47 , HIS A:62 , HIS A:119	BINDING SITE FOR RESIDUE CU A 712
3	AC3	SOFTWARE	HIS B:62 , HIS B:70 , HIS B:79 , ASP B:82	BINDING SITE FOR RESIDUE ZN B 721
4	AC4	SOFTWARE	HIS B:45 , HIS B:47 , HIS B:62 , HIS B:119	BINDING SITE FOR RESIDUE CU B 722
5	AC5	SOFTWARE	HIS C:62 , HIS C:70 , HIS C:79 , ASP C:82	BINDING SITE FOR RESIDUE ZN C 731
6	AC6	SOFTWARE	HIS C:45 , HIS C:47 , HIS C:62 , HIS C:119	BINDING SITE FOR RESIDUE CU C 732
7	AC7	SOFTWARE	HIS D:62 , HIS D:70 , HIS D:79 , ASP D:82	BINDING SITE FOR RESIDUE ZN D 741
8	AC8	SOFTWARE	HIS D:45 , HIS D:47 , HIS D:62 , HIS D:119	BINDING SITE FOR RESIDUE CU D 742
9	AC9	SOFTWARE	GLU B:22 , HIS B:29 , HOH B:832 , GLN C:68 , HOH C:822	BINDING SITE FOR RESIDUE ACT B 701

Asymmetric Unit

No.	Residues
1	A:56	-	A:145
2	B:56	-	B:145
3	C:56	-	C:145
4	D:56	-	D:145

(no "Cis Peptide Bond" information available for 1TO5)

(no "SAP(SNP)/Variant" information available for 1TO5)

Asymmetric 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_SCHMA	43-53	4	A:43-53 B:43-53 C:43-53 D:43-53
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_SCHMA	137-148	4	A:137-147 B:137-147 C:137-147 D:137-147

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_1	PS00087	Copper/Zinc superoxide dismutase signature 1.	SODC_SCHMA	43-53	2	A:43-53 B:43-53 - -
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_SCHMA	137-148	2	A:137-147 B:137-147 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_1	PS00087	Copper/Zinc superoxide dismutase signature 1.	SODC_SCHMA	43-53	2	- - C:43-53 D:43-53
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_SCHMA	137-148	2	- - C:137-147 D:137-147

Biological Unit 3 (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_SCHMA	43-53	4	A:43-53 B:43-53 C:43-53 D:43-53
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_SCHMA	137-148	4	A:137-147 B:137-147 C:137-147 D:137-147

(no "Exon" information available for 1TO5)

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:156
 aligned with SODC_SCHMA | Q01137 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:156
                               1                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
           SODC_SCHMA     - ---MKAVCVMTGTAGVKGVVKFTQETDNGPVHVHAEFSGLKAGKHGFHVHEFGDTTNGCTSAGAHFNPTKQEHGAPEDSIRHVGDLGNVVAGADGNAVYNATDKLISLNGSHSIIGRTMVIHENEDDLGRGGHELSKVTGNAGGRLACGVIGLAAE 153
               SCOP domains d1to5a_ A: Cu,Zn superoxide dismutase, SOD                                                                                                                   SCOP domains
               CATH domains 1to5A00 A:-3-153  [code=2.60.40.200, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eeeeeeee......eeeeeeee....eeeeeeee........hhhhh.....................eeeeeee.....eeeeeee..............eeeee......................eeeeee.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1to5 A  -3 GSNMKAVCVMTGTAGVKGVVKFTQETDNGPVHVHAEFSGLKAGKHGFHVHEFGDTTNGCTSAGAHFNPTKQEHGAPEDSIRHVGDLGNVVAGADGNAVYNATDKLISLNGSHSIIGRSMVIHENEDDLGRGGHELSKVTGNAGGRLACGVVGLAAE 153
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
                             -1|                                                                                                                                                        
                               1

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with SODC_SCHMA | Q01137 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:156
                               1                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
           SODC_SCHMA     - ---MKAVCVMTGTAGVKGVVKFTQETDNGPVHVHAEFSGLKAGKHGFHVHEFGDTTNGCTSAGAHFNPTKQEHGAPEDSIRHVGDLGNVVAGADGNAVYNATDKLISLNGSHSIIGRTMVIHENEDDLGRGGHELSKVTGNAGGRLACGVIGLAAE 153
               SCOP domains d1to5b_ B: Cu,Zn superoxide dismutase, SOD                                                                                                                   SCOP domains
               CATH domains 1to5B00 B:-3-153  [code=2.60.40.200, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eeeeeee.......eeeeeeee....eeeeeeee..................................eeeeeee.....eeeeeee.....hhhhh....eeeee..........hhhhh.......eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1to5 B  -3 GSNMKAVCVMTGTAGVKGVVKFTQETDNGPVHVHAEFSGLKAGKHGFHVHEFGDTTNGCTSAGAHFNPTKQEHGAPEDSIRHVGDLGNVVAGADGNAVYNATDKLISLNGSHSIIGRSMVIHENEDDLGRGGHELSKVTGNAGGRLACGVVGLAAE 153
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
                             -1|                                                                                                                                                        
                               1

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with SODC_SCHMA | Q01137 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:156
                               1                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
           SODC_SCHMA     - ---MKAVCVMTGTAGVKGVVKFTQETDNGPVHVHAEFSGLKAGKHGFHVHEFGDTTNGCTSAGAHFNPTKQEHGAPEDSIRHVGDLGNVVAGADGNAVYNATDKLISLNGSHSIIGRTMVIHENEDDLGRGGHELSKVTGNAGGRLACGVIGLAAE 153
               SCOP domains d1to5c_ C: Cu,Zn superoxide dismutase, SOD                                                                                                                   SCOP domains
               CATH domains 1to5C00 C:-3-153  [code=2.60.40.200, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee....eeeeeee.......eeeeeeee....eeeeeeee........hhhhh.....................eeeeeee.....eeeeeee..............eeeee......................eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1to5 C  -3 GSNMKAVCVMTGTAGVKGVVKFTQETDNGPVHVHAEFSGLKAGKHGFHVHEFGDTTNGCTSAGAHFNPTKQEHGAPEDSIRHVGDLGNVVAGADGNAVYNATDKLISLNGSHSIIGRSMVIHENEDDLGRGGHELSKVTGNAGGRLACGVVGLAAE 153
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
                             -1|                                                                                                                                                        
                               1

Chain D from PDB  Type:PROTEIN  Length:156
 aligned with SODC_SCHMA | Q01137 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:156
                               1                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
           SODC_SCHMA     - ---MKAVCVMTGTAGVKGVVKFTQETDNGPVHVHAEFSGLKAGKHGFHVHEFGDTTNGCTSAGAHFNPTKQEHGAPEDSIRHVGDLGNVVAGADGNAVYNATDKLISLNGSHSIIGRTMVIHENEDDLGRGGHELSKVTGNAGGRLACGVIGLAAE 153
               SCOP domains d1to5d_ D: Cu,Zn superoxide dismutase, SOD                                                                                                                   SCOP domains
               CATH domains 1to5D00 D:-3-153  [code=2.60.40.200, no name defined]                                                                                                        CATH domains
           Pfam domains (1) -----Sod_Cu-1to5D01 D:3-148                                                                                                                            ----- Pfam domains (1)
           Pfam domains (2) -----Sod_Cu-1to5D02 D:3-148                                                                                                                            ----- Pfam domains (2)
           Pfam domains (3) -----Sod_Cu-1to5D03 D:3-148                                                                                                                            ----- Pfam domains (3)
           Pfam domains (4) -----Sod_Cu-1to5D04 D:3-148                                                                                                                            ----- Pfam domains (4)
         Sec.struct. author ....eeeeee......eeeeeee.......eeeeeeee....eeeeeeee..................................eeeeeee.....eeeeeee.....hhhhh....eeeee..........hhhhhh......eeeeee.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1to5 D  -3 GSNMKAVCVMTGTAGVKGVVKFTQETDNGPVHVHAEFSGLKAGKHGFHVHEFGDTTNGCTSAGAHFNPTKQEHGAPEDSIRHVGDLGNVVAGADGNAVYNATDKLISLNGSHSIIGRSMVIHENEDDLGRGGHELSKVTGNAGGRLACGVVGLAAE 153
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
                             -1|                                                                                                                                                        
                               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 '\|'

Asymmetric 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)

Blood fluke (Schistosoma mansoni) [TaxId: 6183] (2)

1a	d1to5a_	A:
1b	d1to5b_	B:
1c	d1to5c_	C:
1d	d1to5d_	D:

Asymmetric 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)

Schistosoma mansoni. Organism_taxid: 6183. (2)

1a	1to5A00	A:-3-153
1b	1to5B00	B:-3-153
1c	1to5C00	C:-3-153
1d	1to5D00	D:-3-153

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Sod_Cu (71)

Schistosoma mansoni (Blood fluke) (1)

1a	Sod_Cu-1to5D01	D:3-148
1b	Sod_Cu-1to5D02	D:3-148
1c	Sod_Cu-1to5D03	D:3-148
1d	Sod_Cu-1to5D04	D:3-148

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SODC_SCHMA | Q01137)

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: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:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
	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: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: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.

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1to4	HIGHER RESOLUTION STRUCTURE

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SS Bonds (4, 4)

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