1Z9P - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

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Title :   X-RAY STRUCTURE OF A CU-ZN SUPEROXIDE DISMUTASE FROM HAEMOPHILUS DUCREYI

Authors :   K. Djinovic Carugo, I. Toeroe

Date :   04 Apr 05 (Deposition) - 12 Sep 06 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Cu-Zn Sod, Sod, Metalloenzymes, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Toro, C. Petrutz, F. Pacello, M. D'Orazio, A. Battistoni, K. Djinovic-Carugo
Structural Basis Of Heme Binding In The Cu, Zn Superoxide Dismutase From Haemophilus Ducreyi.
J. Mol. Biol. V. 386 406 2009
PubMed-ID: 19103206 | Reference-DOI: 10.1016/J.JMB.2008.12.004

Molecule 1 - SUPEROXIDE DISMUTASE [CU-ZN]
	Chains	:	A, B
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHEN-1
	Expression System Strain	:	71/18
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 45-199
	Gene	:	SODC
	Organism Scientific	:	HAEMOPHILUS DUCREYI
	Organism Taxid	:	730
	Other Details	:	MATURE PROTEIN WITHOUT BOUND HAEM

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:70 , HIS A:72 , HIS A:95 , HIS A:151	BINDING SITE FOR RESIDUE CU A 200
2	AC2	SOFTWARE	HIS A:95 , HIS A:104 , HIS A:113 , ASP A:116	BINDING SITE FOR RESIDUE ZN A 201
3	AC3	SOFTWARE	HIS B:70 , HIS B:72 , HIS B:95 , HIS B:151	BINDING SITE FOR RESIDUE CU B 200
4	AC4	SOFTWARE	HIS B:95 , HIS B:104 , HIS B:113 , ASP B:116	BINDING SITE FOR RESIDUE ZN B 201

Asymmetric/Biological Unit

No.	Residues
1	A:77	-	A:173
2	B:77	-	B:173

Asymmetric/Biological Unit

No.	Residues
1	His A:160	-	Pro A:161
2	His B:160	-	Pro B:161

(no "SAP(SNP)/Variant" information available for 1Z9P)

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_HAEDU	90-100	2	A:68-78 B:68-78
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_HAEDU	187-198	2	A:165-176 B:165-176

(no "Exon" information available for 1Z9P)

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
	(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:155
 aligned with SODC_HAEDU | Q59452 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:155
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194     
           SODC_HAEDU    45 EKIVVPVQQLDPQNGNKDVGTVEITESAYGLVFTPKLHDLAHGLHGFHIHEKPSCEPKEKDGKLVAGLGAGGHWDPKQTQKHGYPWSDDAHMGDLPALFVMHDGSATTPVLAPRLKKLAEVKGHSLMIHAGGDNHSDHPAPLGGGGPRMACGVIK 199
               SCOP domains d1z9pa_ A: Cu,Zn superoxide dismutase, SOD                                                                                                                  SCOP domains
               CATH domains 1z9pA00 A:23-177  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeeeeeee..eeeeeeee.....eee.eeee.......eee..eee.hhhhh..........................eee.........eee....hhhhhh.eeeeee..........hhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1--------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9p A  23 EKIVVPVQQLDPQNGNKDVGTVEITESAYGLVFTPKLHDLAHGLHGFHIHEKPSCEPKEKDGKLVAGLGAGGHWDPKQTQKHGYPWSDDAHMGDLPALFVMHDGSATTPVLAPRLKKLAEVKGHSLMIHAGGDNHSDHPAPLGGGGPRMACGVIK 177
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with SODC_HAEDU | Q59452 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:155
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194     
           SODC_HAEDU    45 EKIVVPVQQLDPQNGNKDVGTVEITESAYGLVFTPKLHDLAHGLHGFHIHEKPSCEPKEKDGKLVAGLGAGGHWDPKQTQKHGYPWSDDAHMGDLPALFVMHDGSATTPVLAPRLKKLAEVKGHSLMIHAGGDNHSDHPAPLGGGGPRMACGVIK 199
               SCOP domains d1z9pb_ B: Cu,Zn superoxide dismutase, SOD                                                                                                                  SCOP domains
               CATH domains 1z9pB00 B:23-177  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
           Pfam domains (1) Sod_Cu-1z9pB01 B:23-176                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) Sod_Cu-1z9pB02 B:23-176                                                                                                                                   - Pfam domains (2)
         Sec.struct. author .eeeeeeee.......eeeeeeeeeee..eeeeeeee.....eee.eeee.......eee..eee.hhhhh..........................eee.........eee....hhhhh..eeeeee..........hhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1--------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9p B  23 EKIVVPVQQLDPQNGNKDVGTVEITESAYGLVFTPKLHDLAHGLHGFHIHEKPSCEPKEKDGKLVAGLGAGGHWDPKQTQKHGYPWSDDAHMGDLPALFVMHDGSATTPVLAPRLKKLAEVKGHSLMIHAGGDNHSDHPAPLGGGGPRMACGVIK 177
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

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(

)

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)

Haemophilus ducreyi [TaxId: 730] (2)

1a	d1z9pa_	A:
1b	d1z9pb_	B:

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)

Haemophilus ducreyi. Organism_taxid: 730. (2)

1a	1z9pA00	A:23-177
1b	1z9pB00	B:23-177

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Sod_Cu (71)

Haemophilus ducreyi (2)

1a	Sod_Cu-1z9pB01	B:23-176
1b	Sod_Cu-1z9pB02	B:23-176

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SODC_HAEDU | Q59452)

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
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
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		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		His A:160 - Pro A:161	[ RasMol ]
		His B:160 - Pro B:161	[ RasMol ]

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	1z9p
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	SODC_HAEDU \| Q59452
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	1.15.1.1
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	SODC_HAEDU \| Q59452	:	1z9n

1bzo	THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY
1yai	X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE
2aps	CU/ZN SUPEROXIDE DISMUTASE FROM ACTINOBACILLUS PLEUROPNEUMONIAE

Description

Compounds

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

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