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(-) Description

Title :  SUPEROXIDE DISMUTASE FROM AEROPYRUM PERNIX K1, APO-FORM
 
Authors :  T. Nakamura, K. Uegaki
Date :  30 Jun 10  (Deposition) - 02 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Superoxide Dismutase, Cambialistic, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nakamura, K. Torikai, K. Uegaki, J. Morita, K. Machida, A. Suzuki, Y. Kawata
Crystal Structure Of The Cambialistic Superoxide Dismutase From Aeropyrum Pernix K1 - Insights Into The Enzyme Mechanism And Stability
Febs J. V. 278 598 2011
PubMed-ID: 21182595  |  Reference-DOI: 10.1111/J.1742-4658.2010.07977.X

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [MN/FE]
    Chains: A, B, C, D
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APE0741
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: K1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 26)

Asymmetric/Biological Unit (1, 26)
No.NameCountTypeFull Name
1EDO26Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:11 , LEU A:12 , TYR A:14 , TYR A:16 , HOH A:311BINDING SITE FOR RESIDUE EDO A 215
02AC2SOFTWAREGLU A:20 , ILE B:24 , LEU B:173 , GLN B:174 , EDO B:217 , HOH B:424BINDING SITE FOR RESIDUE EDO A 216
03AC3SOFTWAREASN A:15 , ASN A:17 , EDO B:216 , EDO B:217BINDING SITE FOR RESIDUE EDO A 217
04AC4SOFTWAREILE A:23 , MET A:28 , HIS A:31 , PHE A:82 , ALA A:170 , TYR A:182BINDING SITE FOR RESIDUE EDO A 218
05AC5SOFTWAREHIS A:35 , THR A:38 , HOH A:259 , HOH A:290 , HOH A:447 , ASN C:177BINDING SITE FOR RESIDUE EDO A 219
06AC6SOFTWARELEU A:47 , GLU A:51 , HOH A:396 , HOH A:601 , GLN B:107 , ARG B:143BINDING SITE FOR RESIDUE EDO A 220
07AC7SOFTWAREHIS A:53 , HOH A:271 , HOH A:538 , ALA B:116 , LEU B:117 , ALA B:120BINDING SITE FOR RESIDUE EDO A 221
08AC8SOFTWAREARG A:143 , ILE A:144 , HOH A:508 , LEU B:47 , PHE B:69BINDING SITE FOR RESIDUE EDO A 222
09AC9SOFTWAREGLY A:127 , GLU A:168 , ARG A:179 , HOH A:567 , TRP C:167BINDING SITE FOR RESIDUE EDO A 223
10BC1SOFTWAREPRO B:11 , LEU B:12 , TYR B:14 , TYR B:16 , HIS B:32 , HOH B:272BINDING SITE FOR RESIDUE EDO B 215
11BC2SOFTWAREEDO A:217 , PRO B:21 , ASN B:185 , EDO B:217 , HOH B:221BINDING SITE FOR RESIDUE EDO B 216
12BC3SOFTWAREASN A:17 , GLU A:20 , EDO A:216 , EDO A:217 , HOH A:300 , GLN B:174 , EDO B:216 , HOH B:464BINDING SITE FOR RESIDUE EDO B 217
13BC4SOFTWAREALA B:64 , ASP B:68 , HOH B:225 , HOH B:257 , ASP C:61BINDING SITE FOR RESIDUE EDO B 218
14BC5SOFTWAREGLU B:148 , LYS B:149 , GLU D:148 , LYS D:149BINDING SITE FOR RESIDUE EDO B 219
15BC6SOFTWAREVAL B:125 , GLY B:127 , GLU B:168 , ARG B:179 , HOH B:336 , HOH B:513 , TRP D:167 , HOH D:293 , HOH D:586BINDING SITE FOR RESIDUE EDO B 220
16BC7SOFTWAREGLU A:148 , GLU C:148 , EDO C:218BINDING SITE FOR RESIDUE EDO C 215
17BC8SOFTWAREALA B:64 , ARG B:67 , ASP B:68 , HOH B:248 , ALA C:64 , ARG C:67 , ASP C:68 , HOH C:263BINDING SITE FOR RESIDUE EDO C 216
18BC9SOFTWAREGLN C:107 , PHE C:108 , LEU C:142 , ARG C:143 , HOH C:284 , HOH C:289 , HOH C:374BINDING SITE FOR RESIDUE EDO C 217
19CC1SOFTWAREVAL A:128 , LYS A:149 , GLU C:126 , GLY C:127 , VAL C:128 , GLU C:148 , LYS C:149 , EDO C:215 , HOH C:400BINDING SITE FOR RESIDUE EDO C 218
20CC2SOFTWARETYR C:7 , GLU C:8 , HIS C:76 , HOH C:477BINDING SITE FOR RESIDUE EDO C 219
21CC3SOFTWAREPRO D:11 , LEU D:12 , TYR D:14 , TYR D:16BINDING SITE FOR RESIDUE EDO D 215
22CC4SOFTWAREASN B:177 , LYS D:34 , HIS D:35 , THR D:38 , HOH D:266 , HOH D:293 , HOH D:569 , HOH D:611BINDING SITE FOR RESIDUE EDO D 216
23CC5SOFTWARELYS D:55 , GLU D:57BINDING SITE FOR RESIDUE EDO D 217
24CC6SOFTWAREPRO D:96 , GLY D:97 , GLY D:98 , TRP D:192 , ASP D:193 , GLU D:196BINDING SITE FOR RESIDUE EDO D 218
25CC7SOFTWAREHIS B:35 , GLU D:168 , TYR D:171 , TYR D:172 , ASN D:177 , HOH D:270 , HOH D:387BINDING SITE FOR RESIDUE EDO D 219
26CC8SOFTWAREGLY D:56 , ILE D:58 , GLN D:59 , HOH D:239BINDING SITE FOR RESIDUE EDO D 220

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AK1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:20 -Pro A:21
2Glu B:20 -Pro B:21
3Glu C:20 -Pro C:21
4Glu D:20 -Pro D:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AK1)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_AERPE165-172
 
 
 		  4A:165-172
B:165-172
C:165-172
D:165-172

(-) Exons   (0, 0)

(no "Exon" information available for 3AK1)

(-) 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:212
 aligned with SODF_AERPE | Q9Y8H8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           SODF_AERPE     1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLL 212
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ak1 A   1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLL 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with SODF_AERPE | Q9Y8H8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           SODF_AERPE     1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLLP 213
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ak1 B   1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLLP 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain C from PDB  Type:PROTEIN  Length:213
 aligned with SODF_AERPE | Q9Y8H8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           SODF_AERPE     1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLLP 213
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ak1 C   1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLLP 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain D from PDB  Type:PROTEIN  Length:212
 aligned with SODF_AERPE | Q9Y8H8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           SODF_AERPE     1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLL 212
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee......eeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ak1 D   1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLL 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (0, 0)

(no "SCOP Domain" information available for 3AK1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AK1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AK1)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SODF_AERPE | Q9Y8H8)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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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  3ak1
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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_AERPE | Q9Y8H8: 3ak2 3ak3

(-) Related Entries Specified in the PDB File

3ak2 SAME PROTEIN, MN-BOUND FORM
3ak3 SAME PROTEIN, FE-BOUND FORM