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(-) Description

Title :  X-RAY STRUCTURE OF THE IRON SUPEROXIDE DISMUTASE FROM PSEUDOALTEROMONAS HALOPLANKTIS (CRYSTAL FORM I)
 
Authors :  A. Merlino, I. Russo Krauss, B. Rossi, M. Conte, A. Vergara, F. Sica
Date :  25 Jan 10  (Deposition) - 08 Sep 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cold Adaptation, Superoxide Dismutase, Flexibility, Thermal Stability, Psychrophilic Protein, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Merlino, I. Russo Krauss, I. Castellano, E. De Vendittis, B. Rossi, M. Conte, A. Vergara, F. Sica
Structure And Flexibility In Cold-Adapted Iron Superoxide Dismutases: The Case Of The Enzyme Isolated From Pseudoalteromonas Haloplanktis.
J. Struct. Biol. V. 172 343 2010
PubMed-ID: 20732427  |  Reference-DOI: 10.1016/J.JSB.2010.08.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IRON SUPEROXIDE DISMUTASE
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PSHAA1215, SODB
    Organism Scientific: PSEUDOALTEROMONAS HALOPLANKTIS
    Organism Taxid: 326442
    Strain: TAC 125

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2TRE2Ligand/IonTREHALOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:116 , ASN A:117 , PHE A:118 , ASN A:137 , SER A:139 , HOH A:1052 , HOH A:1120 , HOH A:1169 , HOH A:1170 , HOH A:1179 , HOH A:1197 , HOH A:1205 , GLY B:61 , GLY B:62 , HOH B:1135BINDING SITE FOR RESIDUE TRE A 8000
2AC2SOFTWAREHIS A:26 , HIS A:73 , ASP A:157 , HIS A:161 , HOH A:1039BINDING SITE FOR RESIDUE FE A 5000
3AC3SOFTWAREGLY A:61 , GLY A:62 , ASN A:65 , ASN B:116 , ASN B:117 , PHE B:118 , ASN B:137 , SER B:139 , HOH B:1003 , HOH B:1044 , HOH B:1050 , HOH B:1051 , HOH B:1052 , HOH B:1063 , HOH B:1122 , HOH B:1146 , HOH B:1189BINDING SITE FOR RESIDUE TRE B 8001
4AC4SOFTWAREHIS B:26 , HIS B:73 , ASP B:157 , HIS B:161 , HOH B:1054BINDING SITE FOR RESIDUE FE B 5001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LIO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:15 -Pro A:16
2Glu B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LIO)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_PSEHT157-164
 		  2A:157-164
B:157-164

(-) Exons   (0, 0)

(no "Exon" information available for 3LIO)

(-) Sequences/Alignments

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:192
 aligned with SODF_PSEHT | P84612 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
           SODF_PSEHT     1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
               SCOP domains d3lioa1 A:1-82 automated matches                                                  d3lioa2 A:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lio A   1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with SODF_PSEHT | P84612 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
           SODF_PSEHT     1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
               SCOP domains d3liob1 B:1-82 automated matches                                                  d3liob2 B:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Sod_Fe_N-3lioB03 B:1-81                                                          ----Sod_Fe_C-3lioB01 B:86-191                                                                                 - Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-3lioB04 B:1-81                                                          ----Sod_Fe_C-3lioB02 B:86-191                                                                                 - Pfam domains (2)
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lio B   1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LIO)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Sod_Fe_C] (46)
(-)
Clan: no clan defined [family: Sod_Fe_N] (46)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SODF_PSEHT | P84612)
molecular function
    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: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.

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  1.15.1.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        SODF_PSEHT | P84612: 3lj9 3ljf 4l2a 4l2b 4l2c 4l2d

(-) Related Entries Specified in the PDB File

3lj9 X-RAY STRUCTURE OF THE IRON SUPEROXIDE DISMUTASE FROM PSEUDOALTEROMONAS HALOPLANKTIS IN COMPLEX WITH SODIUM AZIDE
3ljf THE X-RAY STRUCTURE OF IRON SUPEROXIDE DISMUTASE FROM PSEUDOALTEROMONAS HALOPLANKTIS (CRYSTAL FORM II)