1BZO - JenaLib

Title :   THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.

Authors :   D. Bordo, D. Matak, K. Djinovic-Carugo, C. Rosano, A. Pesce, M. Bolognesi, M. E. Stroppolo, M. Falconi, A. Battistoni, A. Desideri

Date :   02 Nov 98 (Deposition) - 09 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Monomeric Cu, Zn Superoxide Dismutase, Protein-Subunit Recognition, Protein Electrostatic, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Bordo, D. Matak, K. Djinovic-Carugo, C. Rosano, A. Pesce, M. Bolognesi, M. E. Stroppolo, M. Falconi, A. Battistoni, A. Desideri
Evolutionary Constraints For Dimer Formation In Prokaryotic Cu, Zn Superoxide Dismutase.
J. Mol. Biol. V. 285 283 1999
PubMed-ID: 9878406 | Reference-DOI: 10.1006/JMBI.1998.2267
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (6, 6)

Asymmetric Unit (6, 6)

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 151
2	AC2	SOFTWARE	HIS A:44 , HIS A:46 , HIS A:61 , HIS A:118	BINDING SITE FOR RESIDUE CU A 152
3	AC3	SOFTWARE	ASP A:76	BINDING SITE FOR RESIDUE IUM A 502
4	AC4	SOFTWARE	GLU A:53B	BINDING SITE FOR RESIDUE IUM A 559
5	CU	AUTHOR	HIS A:44 , HIS A:46 , HIS A:61 , HIS A:118	ACTIVE SITE CU,ZN COORDINATION SPHERE. HIS44, HIS46, HIS61 AND HIS118 ARE COORDINATE TO THE COPPER CATALYTIC ION, WHILE HIS61, HIS69, HIS78 AND ASP81 ARE COORDINATED TO THE ZINC ION
6	ZN	AUTHOR	HIS A:61 , HIS A:69 , HIS A:78 , ASP A:81	ACTIVE SITE CU,ZN COORDINATION SPHERE. HIS44, HIS46, HIS61 AND HIS118 ARE COORDINATE TO THE COPPER CATALYTIC ION, WHILE HIS61, HIS69, HIS78 AND ASP81 ARE COORDINATED TO THE ZINC ION

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	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	1	A:42-52
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_PHOLE	161-172	1	A:136-147

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_PHOLE	65-75	2	A:42-52
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_PHOLE	161-172	2	A:136-147

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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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 d1bzoa_ A: Cu,Zn superoxide dismutase, SOD                                                                                                              SCOP domains
               CATH domains 1bzoA00 A:2-148  [code=2.60.40.200, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......eeeeeeeeee..eeeeeeee.....eee.eeee.......eee..eee..hhh...........................eee.........eee.....hhh...eeeee...........hhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------SOD_CU_ZN_1-------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bzo A   2 QDLTVKMTDLQTGKPVGTIELSQNKYGVVFIPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 148
                                    9B        19        29        39        49    |||53F||      61       |70        80        90       100  ||   113       123 ||    137       147 
                                   9A|                                          53A|||||||             68A                                103|               125|                  
                                    9B                                           53B||||||                                                 107                130                  
                                                                                  53C|||||                                                                                         
                                                                                   53D||||                                                                                         
                                                                                    53E|||                                                                                         
                                                                                     53F||                                                                                         
                                                                                      53G|                                                                                         
                                                                                       53H

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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (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).

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