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(-) Description

Title :  NITRATED HUMAN MANGANESE SUPEROXIDE DISMUTASE
 
Authors :  P. Quint, R. Reutzel, R. Mikulski, R. Mckenna, D. N. Silverman
Date :  20 Jul 05  (Deposition) - 04 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Quint, R. Reutzel, R. Mikulski, R. Mckenna, D. N. Silverman
Crystal Structure Of Nitrated Human Manganese Superoxide Dismutase: Mechanism Of Inactivation.
Free Radic. Biol. Med. V. 40 453 2006
PubMed-ID: 16443160  |  Reference-DOI: 10.1016/J.FREERADBIOMED.2005.08.045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [MN]
    ChainsA
    EC Number1.15.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET
    Expression System Vector TypePLASMID
    GeneSOD2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
2MN1Ligand/IonMANGANESE (II) ION
3NIY1Mod. Amino AcidMETA-NITRO-TYROSINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
3NIY2Mod. Amino AcidMETA-NITRO-TYROSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , NIY A:34 , HIS A:74 , ASP A:159 , HIS A:163 , HOH A:201BINDING SITE FOR RESIDUE MN A 199
2AC2SOFTWAREHIS A:2BINDING SITE FOR RESIDUE K A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ADP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:15 -Pro A:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019364E66VSODM_HUMANPolymorphism5746097AE42V
2UniProtVAR_025898G76RSODM_HUMANPolymorphism4987023AG52R
3UniProtVAR_007165I82TSODM_HUMANPolymorphism1141718AI58T
4UniProtVAR_019365R156WSODM_HUMANPolymorphism5746129AR132W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019364E66VSODM_HUMANPolymorphism5746097AE42V
2UniProtVAR_025898G76RSODM_HUMANPolymorphism4987023AG52R
3UniProtVAR_007165I82TSODM_HUMANPolymorphism1141718AI58T
4UniProtVAR_019365R156WSODM_HUMANPolymorphism5746129AR132W

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_HUMAN183-190  1A:159-166
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_HUMAN183-190  2A:159-166

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003670551bENSE00001872926chr6:160114352-160114177176SODM_HUMAN1-880--
1.2aENST000003670552aENSE00000815316chr6:160113895-160113693203SODM_HUMAN8-76691A:1-5252
1.3ENST000003670553ENSE00000765625chr6:160109274-160109158117SODM_HUMAN76-115401A:52-9140
1.4ENST000003670554ENSE00000765624chr6:160106065-160105886180SODM_HUMAN115-175611A:91-15161
1.5aENST000003670555aENSE00001431742chr6:160103670-160103506165SODM_HUMAN175-222481A:151-19646
1.6bENST000003670556bENSE00001926068chr6:160100330-160100148183SODM_HUMAN-00--

(-) 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: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 d2adpa1 A:1-83 Mn superoxide dismutase (MnSOD)                                     d2adpa2 A:84-196 Mn superoxide dismutase (MnSOD)                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........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: 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:151-196 UniProt: 175-222     Transcript 1 (2)
                 2adp A   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAyVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMAC 196
                                    10        20        30   |    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      
                                                            34-NIY                                                                                                                                                              

   Legend:   → Mismatch (orange background)
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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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ADP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ADP)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 1pl4 1pm9 1qnm 1szx 1var 1xdc 1xil 1zsp 1zte 1zuq 2adq 2gds 2p4k 2qka 2qkc 3c3s 3c3t 5t30 5vf9

(-) Related Entries Specified in the PDB File

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