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(-) Description

Title :  SUPEROXIDE DISMUTASE FROM AEROPYRUM PERNIX K1, MN-BOUND FORM
 
Authors :  T. Nakamura, K. Uegaki
Date :  30 Jun 10  (Deposition) - 02 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
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  (2, 22)

Asymmetric/Biological Unit (2, 22)
No.NameCountTypeFull Name
1EDO18Ligand/Ion1,2-ETHANEDIOL
2MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:31 , HIS A:79 , ASP A:165 , HIS A:169 , HOH A:223BINDING SITE FOR RESIDUE MN A 215
02AC2SOFTWAREGLU A:148 , LYS A:149 , HOH A:280 , HOH A:284 , GLU C:148 , LYS C:149BINDING SITE FOR RESIDUE EDO A 216
03AC3SOFTWAREPRO A:11 , LEU A:12 , TYR A:14 , TYR A:16 , EDO A:220 , HOH A:465BINDING SITE FOR RESIDUE EDO A 217
04AC4SOFTWAREHOH A:331 , HOH A:371 , EDO B:218 , EDO C:218 , EDO D:220BINDING SITE FOR RESIDUE EDO A 218
05AC5SOFTWARELYS A:34 , HIS A:35 , THR A:38 , HOH A:488 , ASN C:177BINDING SITE FOR RESIDUE EDO A 219
06AC6SOFTWARELEU A:9 , PRO A:10 , PRO A:11 , HIS A:32 , EDO A:217BINDING SITE FOR RESIDUE EDO A 220
07AC7SOFTWAREHIS B:31 , HIS B:79 , ASP B:165 , HIS B:169 , HOH B:221BINDING SITE FOR RESIDUE MN B 215
08AC8SOFTWAREPRO B:21 , ASN B:185 , HOH B:271 , HOH B:533BINDING SITE FOR RESIDUE EDO B 216
09AC9SOFTWAREPRO B:11 , LEU B:12 , TYR B:14 , TYR B:16 , HOH B:703BINDING SITE FOR RESIDUE EDO B 217
10BC1SOFTWAREEDO A:218 , GLU B:148 , LYS B:149 , EDO C:218 , GLU D:148BINDING SITE FOR RESIDUE EDO B 218
11BC2SOFTWAREHIS B:35 , TYR B:39 , TRP B:167 , GLU D:168 , ARG D:179 , EDO D:218BINDING SITE FOR RESIDUE EDO B 219
12BC3SOFTWAREHIS C:31 , HIS C:79 , ASP C:165 , HIS C:169 , HOH C:220BINDING SITE FOR RESIDUE MN C 215
13BC4SOFTWAREPRO C:11 , LEU C:12 , TYR C:16 , HIS C:32 , HOH C:436 , HOH C:570 , HOH C:634BINDING SITE FOR RESIDUE EDO C 216
14BC5SOFTWAREGLN C:107 , PHE C:108 , LEU C:142 , ARG C:143 , HOH C:251BINDING SITE FOR RESIDUE EDO C 217
15BC6SOFTWAREEDO A:218 , HOH A:331 , ARG B:67 , EDO B:218 , ARG C:67 , HOH C:255 , HOH C:262 , HOH C:388 , HOH C:672 , GLU D:148BINDING SITE FOR RESIDUE EDO C 218
16BC7SOFTWARETRP A:167 , HOH A:488 , GLY C:127 , GLU C:168 , ARG C:179 , HOH C:555BINDING SITE FOR RESIDUE EDO C 219
17BC8SOFTWAREHIS D:31 , HIS D:79 , ASP D:165 , HIS D:169 , HOH D:221BINDING SITE FOR RESIDUE MN D 215
18BC9SOFTWAREPRO D:96 , GLY D:97 , GLY D:98 , TRP D:192 , GLU D:196BINDING SITE FOR RESIDUE EDO D 216
19CC1SOFTWARETHR C:124 , ASP D:61 , VAL D:62 , ARG D:63 , HOH D:258BINDING SITE FOR RESIDUE EDO D 217
20CC2SOFTWAREPHE B:71 , EDO B:219 , HOH B:316 , VAL D:125 , GLY D:127BINDING SITE FOR RESIDUE EDO D 218
21CC3SOFTWAREPRO D:11 , LEU D:12 , TYR D:14 , TYR D:16BINDING SITE FOR RESIDUE EDO D 219
22CC4SOFTWAREARG A:67 , EDO A:218 , HOH A:371 , GLU C:148 , ARG D:67 , HOH D:237 , HOH D:269 , HOH D:271 , HOH D:403BINDING SITE FOR RESIDUE EDO D 220

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AK2)

(-) 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 3AK2)

(-) 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 3AK2)

(-) 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:211
 aligned with SODF_AERPE | Q9Y8H8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SODF_AERPE     1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYL 211
               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
                 3ak2 A   1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYL 211
                                    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:209
 aligned with SODF_AERPE | Q9Y8H8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:209
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
           SODF_AERPE     5 KRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLLP 213
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee......eeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ak2 B   5 KRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLYLLP 213
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         


Chain C from PDB  Type:PROTEIN  Length:210
 aligned with SODF_AERPE | Q9Y8H8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
           SODF_AERPE     1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLY 210
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee......eeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ak2 C   1 MVSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLY 210
                                    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:209
 aligned with SODF_AERPE | Q9Y8H8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
           SODF_AERPE     2 VSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLY 210
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee......eeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ak2 D   2 VSFKRYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMAPPGKGGGTPGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLTEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYKNDRGSYVENWWNVVNWDDVEKRLEQALNNAKPLY 210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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 3AK2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AK2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AK2)

(-) 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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  3ak2
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 Related Entries

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

UniProtKB/Swiss-Prot
        SODF_AERPE | Q9Y8H8: 3ak1 3ak3

(-) Related Entries Specified in the PDB File

3ak1 SAME PROTEIN, APO-FORM
3ak3 SAME PROTEIN, FE-BOUND FORM