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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOGLOBIN (FERRIC FORM)
 
Authors :  H. Sugimoto, M. Makino, H. Sawai, N. Kawada, K. Yoshizato, Y. Shiro, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 Nov 03  (Deposition) - 08 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Globin, Heme, Oxygen Transport, Oxygen Storage, Ligand Binding, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Sugimoto, M. Makino, H. Sawai, N. Kawada, K. Yoshizato, Y. Shiro
Structural Basis Of Human Cytoglobin For Ligand Binding.
J. Mol. Biol. V. 339 873 2004
PubMed-ID: 15165856  |  Reference-DOI: 10.1016/J.JMB.2004.04.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOGLOBIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCYGB, STAP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHISTOGLOBIN, HGB, STELLATE CELL ACTIVATION- ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:55 , ALA A:56 , TYR A:59 , PHE A:60 , GLN A:77 , HIS A:81 , ARG A:84 , VAL A:85 , ALA A:88 , LEU A:89 , HIS A:113 , LYS A:116 , HIS A:117 , VAL A:119 , TYR A:123 , PHE A:124 , HOH A:201 , HOH A:210BINDING SITE FOR RESIDUE HEM A 191

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V5H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V5H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V5H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V5H)

(-) Exons   (3, 3)

Asymmetric Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002932301ENSE00001246500chr17:74533966-74533482485CYGB_HUMAN1-48481A:21-4828
1.2ENST000002932302ENSE00001058643chr17:74527773-74527542232CYGB_HUMAN48-125781A:48-12578
1.3ENST000002932303ENSE00001118062chr17:74527224-74527061164CYGB_HUMAN126-180551A:126-17146
1.4ENST000002932304ENSE00001193939chr17:74524693-745234611233CYGB_HUMAN180-190110--

(-) 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:151
 aligned with CYGB_HUMAN | Q8WWM9 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:151
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
           CYGB_HUMAN    21 EAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGW 171
               SCOP domains d1v5ha_ A: Cytoglobin                                                                                                                                   SCOP domains
               CATH domains 1v5hA00 A:21-171 Globins                                                                                                                                CATH domains
               Pfam domains --Globin-1v5hA01 A:23-132                                                                                       --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:21-48      -----------------------------------------------------------------------------Exon 1.3  PDB: A:126-171 UniProt: 126-180      Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.2  PDB: A:48-125 UniProt: 48-125                                       ---------------------------------------------- Transcript 1 (2)
                 1v5h A  21 EAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGW 171
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A   (CYGB_HUMAN | Q8WWM9)
molecular function
    GO:0004096    catalase activity    Catalysis of the reaction: 2 hydrogen peroxide = O2 + 2 H2O.
    GO:0047888    fatty acid peroxidase activity    Catalysis of the reaction: 2 H(2)O(2) + H(+) + palmitate = CO(2) + 3 H(2)O + pentadecanal.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008941    nitric oxide dioxygenase activity    Catalysis of the reaction: 2 NO + 2 O2 + NADPH + H+ = 2 nitrate + NADP+.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0019395    fatty acid oxidation    The removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen.
    GO:0032966    negative regulation of collagen biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
    GO:0010764    negative regulation of fibroblast migration    Any process that decreases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium.
    GO:2000490    negative regulation of hepatic stellate cell activation    Any process that stops, prevents or reduces the frequency, rate or extent of hepatic stellate cell activation.
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0050999    regulation of nitric-oxide synthase activity    Any process that modulates the activity of the enzyme nitric-oxide synthase.
    GO:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0006979    response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

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

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        CYGB_HUMAN | Q8WWM91umo 1urv 1ury 1ut0 1ux9 2dc3 3ag0 4b3w

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