1YAI - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE

Authors :   Y. Bourne, S. M. Redford, T. P. Lo, J. A. Tainer, E. D. Getzoff

Date :   03 Feb 96 (Deposition) - 20 Aug 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   Y. Bourne, S. M. Redford, H. M. Steinman, J. R. Lepock, J. A. Tainer, E. D. Getzoff
Novel Dimeric Interface And Electrostatic Recognition In Bacterial Cu, Zn Superoxide Dismutase.
Proc. Natl. Acad. Sci. Usa V. 93 12774 1996
PubMed-ID: 8917495 | Reference-DOI: 10.1073/PNAS.93.23.12774
(for further references see the PDB file header)

Molecule 1 - COPPER, ZINC SUPEROXIDE DISMUTASE
	Chains	:	A, B, C
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	PHSOD
	Expression System Plasmid	:	PPHSOD1LACI
	Expression System Taxid	:	562
	Expression System Vector Type	:	BACTERIAL
	Gene	:	PHSOD
	Organism Scientific	:	PHOTOBACTERIUM LEIOGNATHI
	Organism Taxid	:	658
	Strain	:	MC1061
	Synonym	:	CU, ZN SUPEROXIDE DISMUTASE, CU, ZN SOD

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

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

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:45 , HIS A:47 , HIS A:70 , HIS A:125 , HOH A:154	BINDING SITE FOR RESIDUE CU A 152
02	AC2	SOFTWARE	HIS A:70 , HIS A:79 , HIS A:88 , ASP A:91	BINDING SITE FOR RESIDUE ZN A 153
03	AC3	SOFTWARE	HIS B:45 , HIS B:47 , HIS B:70 , HIS B:125	BINDING SITE FOR RESIDUE CU B 152
04	AC4	SOFTWARE	HIS B:70 , HIS B:79 , HIS B:88 , ASP B:91	BINDING SITE FOR RESIDUE ZN B 153
05	AC5	SOFTWARE	HIS C:45 , HIS C:47 , HIS C:70 , HIS C:125 , HOH C:154	BINDING SITE FOR RESIDUE CU C 152
06	AC6	SOFTWARE	HIS C:70 , HIS C:79 , HIS C:88 , ASP C:91	BINDING SITE FOR RESIDUE ZN C 153
07	CU1	UNKNOWN	HIS A:45 , HIS A:47 , HIS A:70 , HIS A:125	COPPER BINDING SITE.
08	CU2	UNKNOWN	HIS B:45 , HIS B:47 , HIS B:70 , HIS B:125	COPPER BINDING SITE.
09	CU3	UNKNOWN	HIS C:45 , HIS C:47 , HIS C:70 , HIS C:125	COPPER BINDING SITE.
10	ZN1	UNKNOWN	HIS A:70 , HIS A:79 , HIS A:88 , ASP A:91	ZINC BINDING SITE.
11	ZN2	UNKNOWN	HIS B:70 , HIS B:79 , HIS B:88 , ASP B:91	ZINC BINDING SITE.
12	ZN3	UNKNOWN	HIS C:70 , HIS C:79 , HIS C:88 , ASP C:91	ZINC BINDING SITE.

Asymmetric Unit

No.	Residues
1	A:52	-	A:147
2	B:52	-	B:147
3	C:52	-	C:147

Asymmetric Unit

No.	Residues
1	Met A:134	-	Pro A:135
2	Met B:134	-	Pro B:135
3	Met C:134	-	Pro C:135

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

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_1	PS00087	Copper/Zinc superoxide dismutase signature 1.	SODC_PHOLE	65-75	3	A:43-53 B:43-53 C:43-53
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_PHOLE	161-172	3	A:139-150 B:139-150 C:139-150

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_PHOLE	65-75	2	A:43-53 - -
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_PHOLE	161-172	2	A:139-150 - -

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_PHOLE	65-75	2	- B:43-53 C:43-53
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_PHOLE	161-172	2	- B:139-150 C:139-150

(no "Exon" information available for 1YAI)

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:151
 aligned with SODC_PHOLE | P00446 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:151
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 
           SODC_PHOLE    23 QDLTVKMTDLQTGKPVGTIELSQNKYGVVFTPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 173
               SCOP domains d1yaia_ A: Cu,Zn superoxide dismutase, SOD                                                                                                              SCOP domains
               CATH domains 1yaiA00 A:1-151  [code=2.60.40.200, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeeeee..eeeeeeeeee...eeeeeeee.......eee..eee...........................eeeeeeee...eeeeeeeee...hhhhhheeeeeeeee.............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------SOD_CU_ZN_1-------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yai A   1 QDLTVKMTDLQTGKPVGTIELSQNKYGVVFTPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with SODC_PHOLE | P00446 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:151
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 
           SODC_PHOLE    23 QDLTVKMTDLQTGKPVGTIELSQNKYGVVFTPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 173
               SCOP domains d1yaib_ B: Cu,Zn superoxide dismutase, SOD                                                                                                              SCOP domains
               CATH domains 1yaiB00 B:1-151  [code=2.60.40.200, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeeeee..eeeeeeeeee...eeeeeeee.......eee..eee...........................eeeeeeee...eeeeeeeee...hhhhhheeeeeeeee.............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------SOD_CU_ZN_1-------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yai B   1 QDLTVKMTDLQTGKPVGTIELSQNKYGVVFTPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:150
 aligned with SODC_PHOLE | P00446 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:150
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
           SODC_PHOLE    24 DLTVKMTDLQTGKPVGTIELSQNKYGVVFTPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 173
               SCOP domains d1yaic_ C: Cu,Zn superoxide dismutase, SOD                                                                                                             SCOP domains
               CATH domains 1yaiC00 C:2-151  [code=2.60.40.200, no name defined]                                                                                                   CATH domains
           Pfam domains (1) Sod_Cu-1yaiC01 C:2-150                                                                                                                               - Pfam domains (1)
           Pfam domains (2) Sod_Cu-1yaiC02 C:2-150                                                                                                                               - Pfam domains (2)
           Pfam domains (3) Sod_Cu-1yaiC03 C:2-150                                                                                                                               - Pfam domains (3)
         Sec.struct. author .eeeeeeee...eeeeeeeeeee..eeeeeeeeee...eeeeeeee.......eee..eee...........................eeeeeeee...eeeeeeeee...hhhhhheeeeeeeee.............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------SOD_CU_ZN_1-------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yai C   2 DLTVKMTDLQTGKPVGTIELSQNKYGVVFTPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

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(

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Folds(

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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)

Photobacterium leiognathi [TaxId: 553611] (9)

1a	d1yaia_	A:
1b	d1yaib_	B:
1c	d1yaic_	C:

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)

Photobacterium leiognathi. Organism_taxid: 658. Strain: mc1061. (1)

1a	1yaiA00	A:1-151
1b	1yaiB00	B:1-151
1c	1yaiC00	C:2-151

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Sod_Cu (71)

Photobacterium leiognathi (3)

1a	Sod_Cu-1yaiC01	C:2-150
1b	Sod_Cu-1yaiC02	C:2-150
1c	Sod_Cu-1yaiC03	C:2-150

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (SODC_PHOLE | P00446)

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:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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	Cis Peptide Bonds
		Met A:134 - Pro A:135	[ RasMol ]
		Met B:134 - Pro B:135	[ RasMol ]
		Met C:134 - Pro C:135	[ RasMol ]

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	1yai
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	SODC_PHOLE \| P00446	:	1bzo 1ib5 1ibb 1ibd 1ibf 1ibh 1oaj 1oal

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Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (12, 12)

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

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