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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MNSOD Y166F MUTANT
 
Authors :  L. Fan, J. A. Tainer
Date :  06 Jun 03  (Deposition) - 16 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. S. Hearn, L. Fan, J. R. Lepock, J. P. Luba, W. B. Greenleaf, D. E. Cabelli, J. A. Tainer, H. S. Nick, D. N. Silverman
Amino Acid Substitution At The Dimeric Interface Of Human Manganese Superoxide Dismutase
J. Biol. Chem. V. 279 5861 2004
PubMed-ID: 14638684  |  Reference-DOI: 10.1074/JBC.M311310200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [MN], MITOCHONDRIAL
    ChainsA, B, C, D
    EC Number1.15.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRC99A
    Expression System StrainQC774
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    OrganelleMITOCHONDRIA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:74 , ASP A:159 , HIS A:163 , HOH A:201BINDING SITE FOR RESIDUE MN A 200
2AC2SOFTWAREHIS B:26 , HIS B:74 , ASP B:159 , HIS B:163 , HOH B:202BINDING SITE FOR RESIDUE MN B 200
3AC3SOFTWAREHIS C:26 , HIS C:74 , ASP C:159 , HIS C:163 , HOH C:203BINDING SITE FOR RESIDUE MN C 200
4AC4SOFTWAREHIS D:26 , HIS D:74 , ASP D:159 , HIS D:163 , HOH D:204BINDING SITE FOR RESIDUE MN D 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PL4)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 16)

Asymmetric/Biological Unit (4, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019364E66VSODM_HUMANPolymorphism5746097A/B/C/DE42V
2UniProtVAR_025898G76RSODM_HUMANPolymorphism4987023A/B/C/DG52R
3UniProtVAR_007165I82TSODM_HUMANPolymorphism1141718A/B/C/DI58T
4UniProtVAR_019365R156WSODM_HUMANPolymorphism5746129A/B/C/DR132W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_HUMAN183-190
 
 
 
  4A:159-165
B:159-165
C:159-165
D:159-165

(-) Exons   (4, 16)

Asymmetric/Biological Unit (4, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003670551bENSE00001872926chr6:160114352-160114177176SODM_HUMAN1-880--
1.2aENST000003670552aENSE00000815316chr6:160113895-160113693203SODM_HUMAN8-76694A:1-52
B:1-52
C:1-52
D:1-52
52
52
52
52
1.3ENST000003670553ENSE00000765625chr6:160109274-160109158117SODM_HUMAN76-115404A:52-91
B:52-91
C:52-91
D:52-91
40
40
40
40
1.4ENST000003670554ENSE00000765624chr6:160106065-160105886180SODM_HUMAN115-175614A:91-151
B:91-151
C:91-151
D:91-151
61
61
61
61
1.5aENST000003670555aENSE00001431742chr6:160103670-160103506165SODM_HUMAN175-222484A:151-198
B:151-196
C:151-197
D:151-197
48
46
47
47
1.6bENST000003670556bENSE00001926068chr6:160100330-160100148183SODM_HUMAN-00--

(-) 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:198
 aligned with SODM_HUMAN | P04179 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:198
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
           SODM_HUMAN    25 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK 222
               SCOP domains d1pl4a1 A:1-83 Mn superoxide dismutase (MnSOD)                                     d1pl4a2 A:84-198 Mn superoxide dismutase (MnSOD)                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------V---------R-----T-------------------------------------------------------------------------W------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:1-52 UniProt: 8-76 [INCOMPLETE]   --------------------------------------Exon 1.4  PDB: A:91-151 UniProt: 115-175                     ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.3  PDB: A:52-91 UniProt: 76-115  -----------------------------------------------------------Exon 1.5a  PDB: A:151-198 UniProt: 175-222       Transcript 1 (2)
                 1pl4 A   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYFLQYKNVRPDYLKAIWNVINWENVTERYMACKK 198
                                    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:196
 aligned with SODM_HUMAN | P04179 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:196
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214      
           SODM_HUMAN    25 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMAC 220
               SCOP domains d1pl4b1 B:1-83 Mn superoxide dismutase (MnSOD)                                     d1pl4b2 B:84-196 Mn superoxide dismutase (MnSOD)                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------V---------R-----T-------------------------------------------------------------------------W---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:1-52 UniProt: 8-76 [INCOMPLETE]   --------------------------------------Exon 1.4  PDB: B:91-151 UniProt: 115-175                     --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.3  PDB: B:52-91 UniProt: 76-115  -----------------------------------------------------------Exon 1.5a  PDB: B:151-196 UniProt: 175-222     Transcript 1 (2)
                 1pl4 B   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYFLQYKNVRPDYLKAIWNVINWENVTERYMAC 196
                                    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:197
 aligned with SODM_HUMAN | P04179 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:197
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
           SODM_HUMAN    25 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACK 221
               SCOP domains d1pl4c1 C:1-83 Mn superoxide dismutase (MnSOD)                                     d1pl4c2 C:84-197 Mn superoxide dismutase (MnSOD)                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------V---------R-----T-------------------------------------------------------------------------W----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: C:1-52 UniProt: 8-76 [INCOMPLETE]   --------------------------------------Exon 1.4  PDB: C:91-151 UniProt: 115-175                     ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.3  PDB: C:52-91 UniProt: 76-115  -----------------------------------------------------------Exon 1.5a  PDB: C:151-197 UniProt: 175-222      Transcript 1 (2)
                 1pl4 C   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYFLQYKNVRPDYLKAIWNVINWENVTERYMACK 197
                                    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:197
 aligned with SODM_HUMAN | P04179 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:197
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
           SODM_HUMAN    25 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACK 221
               SCOP domains d1pl4d1 D:1-83 Mn superoxide dismutase (MnSOD)                                     d1pl4d2 D:84-197 Mn superoxide dismutase (MnSOD)                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Sod_Fe_N-1pl4D05 D:1-82                                                           ----Sod_Fe_C-1pl4D01 D:87-193                                                                                  ---- Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-1pl4D06 D:1-82                                                           ----Sod_Fe_C-1pl4D02 D:87-193                                                                                  ---- Pfam domains (2)
           Pfam domains (3) Sod_Fe_N-1pl4D07 D:1-82                                                           ----Sod_Fe_C-1pl4D03 D:87-193                                                                                  ---- Pfam domains (3)
           Pfam domains (4) Sod_Fe_N-1pl4D08 D:1-82                                                           ----Sod_Fe_C-1pl4D04 D:87-193                                                                                  ---- Pfam domains (4)
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------V---------R-----T-------------------------------------------------------------------------W----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: D:1-52 UniProt: 8-76 [INCOMPLETE]   --------------------------------------Exon 1.4  PDB: D:91-151 UniProt: 115-175                     ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.3  PDB: D:52-91 UniProt: 76-115  -----------------------------------------------------------Exon 1.5a  PDB: D:151-197 UniProt: 175-222      Transcript 1 (2)
                 1pl4 D   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYFLQYKNVRPDYLKAIWNVINWENVTERYMACK 197
                                    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, 8)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1PL4)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SODM_HUMAN | P04179)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) 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.
biological process
    GO:0003069    acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure    The process in which acetylcholine signaling causes vasodilation, resulting in a change in blood pressure.
    GO:0001315    age-dependent response to reactive oxygen species    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 reactive oxygen species, where the change varies according to the age of the cell or organism.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:1902176    negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of an oxidative stress-induced intrinsic apoptotic signaling pathway.
    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:0032364    oxygen homeostasis    A homeostatic process involved in the maintenance of an internal steady state of oxygen within an organism or cell.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0008217    regulation of blood pressure    Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001836    release of cytochrome c from mitochondria    The process that results in the movement of cytochrome c from the mitochondrial intermembrane space into the cytosol, which is part of the apoptotic signaling pathway and leads to caspase activation.
    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:0000302    response to reactive oxygen species    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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
    GO:0000303    response to superoxide    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 superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SODM_HUMAN | P041791ap5 1ap6 1em1 1ja8 1luv 1luw 1msd 1n0j 1n0n 1pm9 1qnm 1szx 1var 1xdc 1xil 1zsp 1zte 1zuq 2adp 2adq 2gds 2p4k 2qka 2qkc 3c3s 3c3t 5t30 5vf9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PL4)