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Asym./Biol. Unit (Jmol Viewer)

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Title :   CU/ZN SUPEROXIDE DISMUTASE FROM ACTINOBACILLUS PLEUROPNEUMONIAE

Authors :   K. T. Forest, P. R. Langford, J. S. Kroll, E. D. Getzoff

Date :   11 Feb 99 (Deposition) - 25 Feb 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Superoxide Dismutase, Sod, Water-Mediated Dimer, Beta Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. T. Forest, P. R. Langford, J. S. Kroll, E. D. Getzoff
Cu, Zn Superoxide Dismutase Structure From A Microbial Pathogen Establishes A Class With A Conserved Dimer Interface.
J. Mol. Biol. V. 296 145 2000
PubMed-ID: 10656823 | Reference-DOI: 10.1006/JMBI.1999.3448
(for further references see the PDB file header)

Molecule 1 - PROTEIN (CU,ZN SUPEROXIDE DISMUTASE)
	Cellular Location	:	PERIPLASM
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	PERIPLASM
	Expression System Gene	:	SODC
	Expression System Plasmid	:	PJSK157
	Expression System Strain	:	QC779
	Expression System Taxid	:	562
	Gene	:	SODC
	Organism Scientific	:	ACTINOBACILLUS PLEUROPNEUMONIAE
	Organism Taxid	:	715
	Other Details	:	EACH ACTIVE SITE CONTAINS ONE COPPER AND ONE ZINC.
	Synonym	:	SOD

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

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

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:48 , HIS A:50	BINDING SITE FOR RESIDUE CU A 300
2	AC2	SOFTWARE	HIS B:48 , HIS B:50 , HIS B:114 , HOH B:1353	BINDING SITE FOR RESIDUE CU B 500
3	AC3	SOFTWARE	HIS A:85 , HIS A:94 , HIS A:103 , ASP A:106	BINDING SITE FOR RESIDUE ZN A 400
4	AC4	SOFTWARE	HIS A:60 , HIS A:62 , HIS A:85 , HIS A:141	BINDING SITE FOR RESIDUE CU A 402
5	AC5	SOFTWARE	HIS B:85 , HIS B:94 , HIS B:103 , ASP B:106	BINDING SITE FOR RESIDUE ZN B 600
6	AC6	SOFTWARE	HIS B:60 , HIS B:62 , HIS B:85 , HIS B:141	BINDING SITE FOR RESIDUE CU B 602
7	ACT	AUTHOR	HIS A:60 , HIS A:62 , HIS A:85 , HIS A:94 , HIS A:103 , HIS A:141 , HIS B:60 , HIS B:62 , HIS B:85 , HIS B:94 , HIS B:103 , HIS B:141	COPPER AND ZINC ARE LIGATED BY THREE CONSERVED HISTIDINES EACH IN THE ACTIVE SITE OF EACH SUBUNIT.

Asymmetric/Biological Unit

No.	Residues
1	A:67	-	A:163
2	B:67	-	B:163

Asymmetric/Biological Unit

No.	Residues
1	His A:150	-	Pro A:151
2	His B:150	-	Pro B:151

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

Asymmetric/Biological Unit (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_ACTPL	81-91	2	A:58-68 B:58-68
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_ACTPL	178-189	2	A:155-166 B:155-166

(no "Exon" information available for 2APS)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:155
 aligned with SODC_ACTPL | P24702 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:155
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185     
           SODC_ACTPL    36 EKLVVQVQQLDPVKGNKDVGTVEITESAYGLVFTPHLHGLAQGLHGFHIHQNPSCEPKEKDGKLVAGLGAGGHWDPKETKQHGYPWSDNAHLGDLPALFVEHDGSATNPVLAPRLKKLDEVKGHSLMIHEGGDNHSDHPAPLGGGGPRMACGVIK 190
               SCOP domains d2apsa_ A: Cu,Zn superoxide dismutase, SOD                                                                                                                  SCOP domains
               CATH domains 2apsA00 A:13-167  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......eeeeeeeeeee..eeeeeeee.....eee.eeee.......eee.......hhh...........................eee.........eee.....hhhh..eeeeee...........hhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1--------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aps A  13 EKLVVQVQQLDPVKGNKDVGTVEITESAYGLVFTPHLHGLAQGLHGFHIHQNPSCEPKEKDGKLVAGLGAGGHWDPKETKQHGYPWSDNAHLGDLPALFVEHDGSATNPVLAPRLKKLDEVKGHSLMIHEGGDNHSDHPAPLGGGGPRMACGVIK 167
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with SODC_ACTPL | P24702 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:155
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185     
           SODC_ACTPL    36 EKLVVQVQQLDPVKGNKDVGTVEITESAYGLVFTPHLHGLAQGLHGFHIHQNPSCEPKEKDGKLVAGLGAGGHWDPKETKQHGYPWSDNAHLGDLPALFVEHDGSATNPVLAPRLKKLDEVKGHSLMIHEGGDNHSDHPAPLGGGGPRMACGVIK 190
               SCOP domains d2apsb_ B: Cu,Zn superoxide dismutase, SOD                                                                                                                  SCOP domains
               CATH domains 2apsB00 B:13-167  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeeeeeee..eeeeeeee.....eee.eeee.......eee..eee..hhh...........................eee.........eee.....hhhh..eeeeee...........hhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1--------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aps B  13 EKLVVQVQQLDPVKGNKDVGTVEITESAYGLVFTPHLHGLAQGLHGFHIHQNPSCEPKEKDGKLVAGLGAGGHWDPKETKQHGYPWSDNAHLGDLPALFVEHDGSATNPVLAPRLKKLDEVKGHSLMIHEGGDNHSDHPAPLGGGGPRMACGVIK 167
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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)

Actinobacillus pleuropneumoniae [TaxId: 715] (1)

1a	d2apsa_	A:
1b	d2apsb_	B:

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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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)

Actinobacillus pleuropneumoniae. Organism_taxid: 715. (1)

1a	2apsA00	A:13-167
1b	2apsB00	B:13-167

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SODC_ACTPL | P24702)

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/Biological Unit
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	Ligands, Modified Residues, Ions
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		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		His A:150 - Pro A:151	[ RasMol ]
		His B:150 - Pro B:151	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (7, 7)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

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