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(-) Description

Title :  THE X-RAY STRUCTURE OF IRON SUPEROXIDE DISMUTASE FROM PSEUDOALTEROMONAS HALOPLANKTIS (CRYSTAL FORM II)
 
Authors :  A. Merlino, I. Russo Krauss, B. Rossi, M. Conte, A. Vergara, F. Sica
Date :  26 Jan 10  (Deposition) - 08 Sep 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C, B, D
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SODB, PSHAA1215
    Organism Scientific: PSEUDOALTEROMONAS HALOPLANKTIS
    Organism Taxid: 326442
    Strain: TAC 125

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION
2TRE4Ligand/IonTREHALOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2TRE2Ligand/IonTREHALOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2TRE2Ligand/IonTREHALOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:73 , ASP A:157 , HIS A:161 , HOH A:5004BINDING SITE FOR RESIDUE FE A 5000
2AC2SOFTWAREASN A:116 , ASN A:117 , PHE A:118 , ASN A:137 , SER A:139 , HOH A:5130 , HOH A:5179 , HOH A:5340 , HOH A:5376 , GLY B:61 , GLY B:62 , HOH B:5366BINDING SITE FOR RESIDUE TRE A 193
3AC3SOFTWAREHIS C:26 , HIS C:73 , ASP C:157 , HIS C:161 , HOH C:5006BINDING SITE FOR RESIDUE FE C 5002
4AC4SOFTWAREASN C:116 , ASN C:117 , PHE C:118 , ASN C:137 , SER C:139 , HOH C:1720 , HOH C:1727 , HOH C:5191 , GLY D:61 , GLY D:62BINDING SITE FOR RESIDUE TRE C 195
5AC5SOFTWAREHIS B:26 , HIS B:73 , ASP B:157 , HIS B:161 , HOH B:5005BINDING SITE FOR RESIDUE FE B 5001
6AC6SOFTWAREGLY A:61 , GLY A:62 , LYS B:113 , ASN B:116 , ASN B:117 , PHE B:118 , ASN B:137 , HOH B:1736 , HOH B:5180 , HOH B:5252 , HOH B:5269 , HOH B:5337 , HOH B:5379BINDING SITE FOR RESIDUE TRE B 194
7AC7SOFTWAREHIS D:26 , HIS D:73 , ASP D:157 , HIS D:161 , HOH D:1699BINDING SITE FOR RESIDUE FE D 5003
8AC8SOFTWAREGLY C:61 , GLY C:62 , ASN C:65 , LYS D:113 , ASN D:116 , ASN D:117 , PHE D:118 , ASN D:137 , HOH D:1723 , HOH D:1745 , HOH D:5314 , HOH D:5394 , HOH D:5408 , HOH D:5414BINDING SITE FOR RESIDUE TRE D 196

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:15 -Pro A:16
2Glu C:15 -Pro C:16
3Glu B:15 -Pro B:16
4Glu D:15 -Pro D:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_PSEHT157-164
 
 
 		  4A:157-164
B:157-164
C:157-164
D:157-164
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_PSEHT157-164
 
 
 		  2A:157-164
B:157-164
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_PSEHT157-164
 
 
 		  2-
-
C:157-164
D:157-164

(-) Exons   (0, 0)

(no "Exon" information available for 3LJF)

(-) 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: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 d3ljfa1 A:1-82 automated matches                                                  d3ljfa2 A:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ljf 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 d3ljfb1 B:1-82 automated matches                                                  d3ljfb2 B:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ljf B   1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  


Chain C 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 d3ljfc1 C:1-82 automated matches                                                  d3ljfc2 C:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ljf C   1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  


Chain D 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 d3ljfd1 D:1-82 automated matches                                                  d3ljfd2 D:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Sod_Fe_N-3ljfD05 D:1-81                                                          ----Sod_Fe_C-3ljfD01 D:86-191                                                                                 - Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-3ljfD06 D:1-81                                                          ----Sod_Fe_C-3ljfD02 D:86-191                                                                                 - Pfam domains (2)
           Pfam domains (3) Sod_Fe_N-3ljfD07 D:1-81                                                          ----Sod_Fe_C-3ljfD03 D:86-191                                                                                 - Pfam domains (3)
           Pfam domains (4) Sod_Fe_N-3ljfD08 D:1-81                                                          ----Sod_Fe_C-3ljfD04 D:86-191                                                                                 - Pfam domains (4)
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ljf D   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)
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  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, 8)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 8)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  3ljf
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  SODF_PSEHT | P84612
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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: 3lio 3lj9 4l2a 4l2b 4l2c 4l2d

(-) Related Entries Specified in the PDB File

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