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(-) Description

Title :  CRYSTAL STRUCTURE OF A CU-ZN SUPEROXIDE DISMUTASE FROM MYCOBACTERIUM TUBERCULOSIS AT 1.63 RESOLUTION
 
Authors :  K. Djinovic-Carugo, L. Spagnolo, I. Toro
Date :  14 Jul 03  (Deposition) - 27 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cu-Protein, Beta Core, Antioxidant, Metal Binding, Greek Key Beta Barrel, Oxidoreductase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Spagnolo, I. Toro, M. D'Orazio, P. O'Neill, J. Z. Pedersen, O. Carugo, G. Rotilio, A. Battistoni, K. Djinovic-Carugo
Unique Features Of The Sodc-Encoded Superoxide Dismutase From Mycobacterium Tuberculosis, A Fully Functional Copper-Containing Enzyme Lacking Zinc In The Active Site.
J. Biol. Chem. V. 279 33447 2004
PubMed-ID: 15155722  |  Reference-DOI: 10.1074/JBC.M404699200

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [CU-ZN]
    ChainsA
    EC Number1.15.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC19
    Expression System StrainQC871
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 33-240
    GeneSODC OR RV0432 OR MT0447 OR MTCY22G10.29
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:47 , HIS A:49 , HIS A:75 , HIS A:126 , HOH A:448BINDING SITE FOR RESIDUE CU A 172

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:54 -A:165

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:84 -Pro A:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_CU_ZN_2PS00332 Copper/Zinc superoxide dismutase signature 2.SODC_MYCTO226-237  1A:157-168
SODC_MYCTU226-237  1A:157-168
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_CU_ZN_2PS00332 Copper/Zinc superoxide dismutase signature 2.SODC_MYCTO226-237  2A:157-168
SODC_MYCTU226-237  2A:157-168

(-) Exons   (0, 0)

(no "Exon" information available for 1PZS)

(-) Sequences/Alignments

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:171
 aligned with SODC_MYCTO | P9WGE8 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:171
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
           SODC_MYCTO    70 QSLTSTLTAPDGTKVATAKFEFANGYATVTIATTGVGKLTPGFHGLHIHQVGKCEPNSVAPTGGAPGNFLSAGGHYHVPGHTGTPASGDLASLQVRGDGSAMLVTTTDAFTMDDLLSGAKTAIIIHAGADNFANIPPERYVQVNGTPGPDETTLTTGDAGKRVACGVIGSG 240
               SCOP domains d1pzsa_ A: Cu,Zn superoxide dismutase, SOD                                                                                                                                  SCOP domains
               CATH domains 1pzsA00 A:1-171  [code=2.60.40.200, no name defined]                                                                                                                        CATH domains
               Pfam domains --Sod_Cu-1pzsA01 A:3-168                                                                                                                                                --- Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeeeeee..eeeeeeee........eee.eeee...................hhhhh...................eee......eeeeee...hhhhhhh....eeeee.......................hhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_CU_ZN_2 --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pzs A   1 QSLTSTLTAPDGTKVATAKFEFANGYATVTIATTGVGKLTPGFHGLHIHQVGKCEPNSVAPTGGAPGNFLSAGGHYHVPGHTGTPASGDLASLQVRGDGSAMLVTTTDAFTMDDLLSGAKTAIIIHAGADNFANIPPERYVQVNGTPGPDETTLTTGDAGKRVACGVIGSG 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

Chain A from PDB  Type:PROTEIN  Length:171
 aligned with SODC_MYCTU | P9WGE9 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:171
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
           SODC_MYCTU    70 QSLTSTLTAPDGTKVATAKFEFANGYATVTIATTGVGKLTPGFHGLHIHQVGKCEPNSVAPTGGAPGNFLSAGGHYHVPGHTGTPASGDLASLQVRGDGSAMLVTTTDAFTMDDLLSGAKTAIIIHAGADNFANIPPERYVQVNGTPGPDETTLTTGDAGKRVACGVIGSG 240
               SCOP domains d1pzsa_ A: Cu,Zn superoxide dismutase, SOD                                                                                                                                  SCOP domains
               CATH domains 1pzsA00 A:1-171  [code=2.60.40.200, no name defined]                                                                                                                        CATH domains
               Pfam domains --Sod_Cu-1pzsA01 A:3-168                                                                                                                                                --- Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeeeeee..eeeeeeee........eee.eeee...................hhhhh...................eee......eeeeee...hhhhhhh....eeeee.......................hhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_CU_ZN_2 --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pzs A   1 QSLTSTLTAPDGTKVATAKFEFANGYATVTIATTGVGKLTPGFHGLHIHQVGKCEPNSVAPTGGAPGNFLSAGGHYHVPGHTGTPASGDLASLQVRGDGSAMLVTTTDAFTMDDLLSGAKTAIIIHAGADNFANIPPERYVQVNGTPGPDETTLTTGDAGKRVACGVIGSG 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (21, 31)

Asymmetric Unit(hide GO term definitions)
Chain A   (SODC_MYCTU | P9WGE9)
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: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:0004784    superoxide dismutase activity    Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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:0052060    evasion or tolerance by symbiont of host-produced nitric oxide    The process in which an organism avoids the effects of nitric oxide produced as a defense response by the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0052059    evasion or tolerance by symbiont of host-produced reactive oxygen species    The process in which an organism avoids the effects of reactive oxygen species produced as a defense response by the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:0075136    response to host    Any process that results in a change in state or activity of the symbiont or its cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0033194    response to hydroperoxide    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 hydroperoxide stimulus. Hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH.
    GO:0006979    response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    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:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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).
    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.

Chain A   (SODC_MYCTO | P9WGE8)
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

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1eqw CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM CU, ZN SUPEROXIDE DISMUTASE
1eso MONOMERIC CU, ZN SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI
1jcv REDUCED BRIDGE-BROKEN YEAST CU/ZN SUPEROXIDE DISMUTASE LOW TEMPERATURE (-180C) STRUCTURE
1xso THREE-DIMENSIONAL STRUCTURE OF XENOPUS LAEVIS CU, ZN SUPEROXIDE DISMUTASE B DETERMINED BY X-RAY CRYSTALLOGRAPHY AT 1.5 ANGSTROM RESOLUTION.