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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF H2O2 TREATED CU,ZN-SOD

Authors :   S. Ito, T. Ishii, K. Uchida

Date :   29 Aug 07 (Deposition) - 02 Sep 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Metalloprotein, Dismutase, Hydrogen Peroxide, Acetylation, Antioxidant, Copper, Cytoplasm, Metal-Binding, Oxidoreductase, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ito, T. Ishii, K. Uchida
Crystal Structures Of H2O2-Treated Cu, Zn-Superoxide Dismutase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SUPEROXIDE DISMUTASE [CU-ZN]
	Cell	:	ERYTHROCYTE
	Chains	:	A, B
	EC Number	:	1.15.1.1
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	SIGMA-ALDRICH CHEMICAL COMPANY

		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:61 , HIS A:69 , HIS A:78 , ASP A:81	BINDING SITE FOR RESIDUE ZN A 300
2	AC2	SOFTWARE	HIS A:44 , HIS A:46 , HIS A:61 , HIS A:118	BINDING SITE FOR RESIDUE CU A 301
3	AC3	SOFTWARE	HIS B:61 , HIS B:69 , HIS B:78 , ASP B:81	BINDING SITE FOR RESIDUE ZN B 300
4	AC4	SOFTWARE	HIS B:44 , HIS B:46 , HIS B:61 , HIS B:118 , HOH B:532	BINDING SITE FOR RESIDUE CU B 301

Asymmetric/Biological Unit

No.	Residues
1	A:55	-	A:144
2	B:55	-	B:144

(no "Cis Peptide Bond" information available for 2Z7W)

(no "SAP(SNP)/Variant" information available for 2Z7W)

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_BOVIN	43-53	2	A:42-52 B:42-52
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_BOVIN	137-148	2	A:136-147 B:136-147

Asymmetric/Biological Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000032452	1	ENSBTAE00000259570	chr1:2920927-2920763	165	SODC_BOVIN	1-24	24	2	A:1-23 B:1-23	23 23
1.2	ENSBTAT00000032452	2	ENSBTAE00000204052	chr1:2917164-2917074	91	SODC_BOVIN	25-55	31	2	A:24-54 B:24-54	31 31
1.3	ENSBTAT00000032452	3	ENSBTAE00000204053	chr1:2915376-2915307	70	SODC_BOVIN	55-78	24	2	A:54-77 B:54-77	24 24
1.4	ENSBTAT00000032452	4	ENSBTAE00000204054	chr1:2914479-2914362	118	SODC_BOVIN	78-117	40	2	A:77-116 B:77-116	40 40
1.5	ENSBTAT00000032452	5	ENSBTAE00000204055	chr1:2912760-2912336	425	SODC_BOVIN	118-152	35	2	A:117-151 B:117-151	35 35

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:151
 aligned with SODC_BOVIN | P00442 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
           SODC_BOVIN     2 ATKAVCVLKGDGPVQGTIHFEAKGDTVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSKKHGGPKDEERHVGDLGNVTADKNGVAIVDIVDPLISLSGEYSIIGRTMVVHEKPDDLGRGGNEESTKTGNAGSRLACGVIGIAK 152
               SCOP domains d2z7wa_ A: Cu,Zn superoxide dismutase, SOD                                                                                                              SCOP domains
               CATH domains 2z7wA00 A:1-151  [code=2.60.40.200, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeeeee..eeeeeeeee....eeeeeeee........hhhhh.....................eeeeeee....eeeeeeee..............eeeee......................eeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ---- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-23  Exon 1.2  PDB: A:24-54         ----------------------Exon 1.4  PDB: A:77-116 UniProt: 78-117 Exon 1.5  PDB: A:117-151            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.3  PDB: A:54-77  -------------------------------------------------------------------------- Transcript 1 (2)
                 2z7w A   1 ATKAVCVLKGDGPVQGTIHFEAKGDTVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSKKHGGPKDEERHVGDLGNVTADKNGVAIVDIVDPLISLSGEYSIIGRTMVVHEKPDDLGRGGNEESTKTGNAGSRLACGVIGIAK 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_BOVIN | P00442 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
           SODC_BOVIN     2 ATKAVCVLKGDGPVQGTIHFEAKGDTVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSKKHGGPKDEERHVGDLGNVTADKNGVAIVDIVDPLISLSGEYSIIGRTMVVHEKPDDLGRGGNEESTKTGNAGSRLACGVIGIAK 152
               SCOP domains d2z7wb_ B: Cu,Zn superoxide dismutase, SOD                                                                                                              SCOP domains
               CATH domains 2z7wB00 B:1-151  [code=2.60.40.200, no name defined]                                                                                                    CATH domains
           Pfam domains (1) ---Sod_Cu-2z7wB01 B:4-147                                                                                                                          ---- Pfam domains (1)
           Pfam domains (2) ---Sod_Cu-2z7wB02 B:4-147                                                                                                                          ---- Pfam domains (2)
         Sec.struct. author ..eeeeee......eeeeeeeee..eeeeeeeee....eeeeeeee......hhhhhhh.....................eeeeeee.....eeeeeee..............eeeee............hhhhhh....eeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ---- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:1-23  Exon 1.2  PDB: B:24-54         ----------------------Exon 1.4  PDB: B:77-116 UniProt: 78-117 Exon 1.5  PDB: B:117-151            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.3  PDB: B:54-77  -------------------------------------------------------------------------- Transcript 1 (2)
                 2z7w B   1 ATKAVCVLKGDGPVQGTIHFEAKGDTVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSKKHGGPKDEERHVGDLGNVTADKNGVAIVDIVDPLISLSGEYSIIGRTMVVHEKPDDLGRGGNEESTKTGNAGSRLACGVIGIAK 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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)

Cow (Bos taurus) [TaxId: 9913] (23)

1a	d2z7wa_	A:
1b	d2z7wb_	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)

Bovine (Bos taurus) (5)

1a	2z7wA00	A:1-151
1b	2z7wB00	B:1-151

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Sod_Cu (71)

Bos taurus (Bovine) (12)

1a	Sod_Cu-2z7wB01	B:4-147
1b	Sod_Cu-2z7wB02	B:4-147

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SODC_BOVIN | P00442)

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:0051087	chaperone binding	Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
	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:0030346	protein phosphatase 2B binding	Interacting selectively and non-covalently with the enzyme protein phosphatase 2B.
	GO:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0006309	apoptotic DNA fragmentation	The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
	GO:0060088	auditory receptor cell stereocilium organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of auditory hair cells.
	GO:0007569	cell aging	An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0006302	double-strand break repair	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
	GO:0007566	embryo implantation	Attachment of the blastocyst to the uterine lining.
	GO:0006749	glutathione metabolic process	The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
	GO:0060047	heart contraction	The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body.
	GO:0050665	hydrogen peroxide biosynthetic process	The chemical reactions and pathways resulting in the formation of hydrogen peroxide (H2O2), a potentially harmful byproduct of aerobic cellular respiration which can cause damage to DNA.
	GO:0044419	interspecies interaction between organisms	Any process in which an organism has an effect on an organism of a different species.
	GO:0007626	locomotory behavior	The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
	GO:0046716	muscle cell cellular homeostasis	The cellular homeostatic process that preserves a muscle cell in a stable functional or structural state.
	GO:0002262	myeloid cell homeostasis	The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
	GO:0045541	negative regulation of cholesterol biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol.
	GO:0043524	negative regulation of neuron apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
	GO:0060052	neurofilament cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising neurofilaments and their associated proteins.
	GO:0001541	ovarian follicle development	The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
	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:0032287	peripheral nervous system myelin maintenance	The process in which the structure and material content of mature peripheral nervous system myelin is kept in a functional state.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:0001819	positive regulation of cytokine production	Any process that activates or increases the frequency, rate or extent of production of a cytokine.
	GO:0051770	positive regulation of nitric-oxide synthase biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.
	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0000209	protein polyubiquitination	Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
	GO:0072593	reactive oxygen species metabolic process	The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
	GO:0008217	regulation of blood pressure	Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
	GO:0001817	regulation of cytokine production	Any process that modulates the frequency, rate, or extent of production of a cytokine.
	GO:0051881	regulation of mitochondrial membrane potential	Any process that modulates the establishment or extent of the mitochondrial membrane potential, the electric potential existing across the mitochondrial membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
	GO:0040014	regulation of multicellular organism growth	Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
	GO:0045859	regulation of protein kinase activity	Any process that modulates the frequency, rate or extent of protein kinase activity.
	GO:0060087	relaxation of vascular smooth muscle	A negative regulation of smooth muscle contraction resulting in relaxation of vascular smooth muscle. The relaxation is mediated by a decrease in the phosphorylation state of myosin light chain. This can be achieved by removal of calcium from the cytoplasm to the sarcoplasmic reticulum lumen through the action of Ca2+ ATPases leading to a decrease myosin light chain kinase activity, and through calcium-independent pathways leading to a increase in myosin light chain phosphatase activity.
	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:0048678	response to axon injury	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.) as a result of an axon injury stimulus.
	GO:0042493	response to drug	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.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0045471	response to ethanol	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.) as a result of an ethanol stimulus.
	GO:0009408	response to heat	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.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0042542	response to hydrogen peroxide	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.) as a result of a hydrogen peroxide (H2O2) stimulus.
	GO:0010033	response to organic substance	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.) as a result of an organic substance stimulus.
	GO:0000303	response to superoxide	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.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
	GO:0007605	sensory perception of sound	The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	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.
	GO:0019226	transmission of nerve impulse	The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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:0032839	dendrite cytoplasm	All of the contents of a dendrite, excluding the surrounding plasma membrane.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	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:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 2z7w)

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	2z7w
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	1.15.1.1
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2z7u	THE MOST SEVERELY MODIFIED CU,ZN-SOD
2z7y	H2O2 TREATMENT WAS PERFORMED UNDER MILD CONDITION
2z7z	H2O2 TREATMENT WAS PERFORMED COEXISTENT WITH BICARBONATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (5, 10)

Sequences/Alignments

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SCOP Domains (1, 2)

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Pfam Domains (1, 2)

Gene Ontology (66, 66)

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