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(-) Description

Title :  MAPPING PROTEIN MATRIX CAVITIES IN HUMAN CYTOGLOBIN THROUGH XE ATOM BINDING: A CRYSTALLOGRAPHIC INVESTIGATION
 
Authors :  D. De Sanctis, S. Dewilde, A. Pesce, L. Moens, P. Ascenzi, T. Hankeln, T. Burmester, M. Bolognesi
Date :  23 Feb 04  (Deposition) - 01 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxygen Transport, Oxygen Storage/Transport, Heme, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. De Sanctis, S. Dewilde, A. Pesce, L. Moens, P. Ascenzi, T. Hankeln, T. Burmester, M. Bolognesi
Mapping Protein Matrix Cavities In Human Cytoglobin Through Xe Atom Binding
Biochem. Biophys. Res. Commun. V. 316 1217 2004
PubMed-ID: 15044115  |  Reference-DOI: 10.1016/J.BBRC.2004.03.007

(-) Compounds

Molecule 1 - CYTOGLOBIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHISTOGLOBIN, HGB, STELLATE CELL ACTIVATION- ASSOCIATED-PROTEIN, CYGB, STAP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1FC62Ligand/IonHEXACYANOFERRATE(3-)
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3XE7Ligand/IonXENON
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FC61Ligand/IonHEXACYANOFERRATE(3-)
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3XE-1Ligand/IonXENON
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FC61Ligand/IonHEXACYANOFERRATE(3-)
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3XE-1Ligand/IonXENON

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:59 , PHE A:60 , GLN A:77 , HIS A:81 , ARG A:84 , ALA A:88 , ALA A:112 , HIS A:113 , HIS A:117 , VAL A:119 , TYR A:123 , PHE A:124 , HOH A:2007 , HOH A:2011BINDING SITE FOR RESIDUE HEM A1172
2AC2SOFTWAREGLY A:42 , ILE A:45 , MET A:86BINDING SITE FOR RESIDUE XE A1173
3AC3SOFTWARELEU A:89BINDING SITE FOR RESIDUE XE A1174
4AC4SOFTWARETRP A:31 , LEU A:34 , ILE A:45 , MET A:86 , ILE A:131BINDING SITE FOR RESIDUE XE A1175
5AC5SOFTWARELYS A:125 , ARG A:155 , GLY A:156 , TYR A:159 , HOH A:2022 , PHE B:53 , PRO B:54 , SER B:55BINDING SITE FOR RESIDUE FC6 A1176
6AC6SOFTWAREALA A:140 , SER A:141 , TYR B:59 , PHE B:60 , GLN B:77 , LYS B:80 , HIS B:81 , ARG B:84 , VAL B:85 , ALA B:88 , LEU B:89 , HIS B:113 , HIS B:117 , VAL B:119 , PHE B:124 , HOH B:2015BINDING SITE FOR RESIDUE HEM B1172
7AC7SOFTWAREPHE A:53 , PRO A:54 , SER A:55 , LYS B:125 , ARG B:155 , TYR B:159BINDING SITE FOR RESIDUE FC6 B1176

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UX9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UX9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UX9)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.CYGB_HUMAN19-158
 
  2A:19-158
B:19-158
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.CYGB_HUMAN19-158
 
  1A:19-158
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.CYGB_HUMAN19-158
 
  1-
B:19-158

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002932301ENSE00001246500chr17:74533966-74533482485CYGB_HUMAN1-48482A:18-48
B:18-48
31
31
1.2ENST000002932302ENSE00001058643chr17:74527773-74527542232CYGB_HUMAN48-125782A:48-125
B:48-125
78
78
1.3ENST000002932303ENSE00001118062chr17:74527224-74527061164CYGB_HUMAN126-180552A:126-171
B:126-171
46
46
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:154
 aligned with CYGB_HUMAN | Q8WWM9 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:154
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167    
           CYGB_HUMAN    18 ELSEAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGW 171
               SCOP domains d1ux9a_ A: Cytoglobin                                                                                                                                      SCOP domains
               CATH domains 1ux9A00 A:18-171 Globins                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:19-158 UniProt: 19-158                                                                                                       ------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:18-48         -----------------------------------------------------------------------------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)
                 1ux9 A  18 ELSEAERKAVQAMWARLYANSEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHASRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGW 171
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167    

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with CYGB_HUMAN | Q8WWM9 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:154
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167    
           CYGB_HUMAN    18 ELSEAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGW 171
               SCOP domains d1ux9b_ B: Cytoglobin                                                                                                                                      SCOP domains
               CATH domains 1ux9B00 B:18-171 Globins                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: B:19-158 UniProt: 19-158                                                                                                       ------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:18-48         -----------------------------------------------------------------------------Exon 1.3  PDB: B:126-171 UniProt: 126-180      Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2  PDB: B:48-125 UniProt: 48-125                                       ---------------------------------------------- Transcript 1 (2)
                 1ux9 B  18 ELSEAERKAVQAMWARLYANSEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHASRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGW 171
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167    

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1UX9)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        CYGB_HUMAN | Q8WWM91umo 1urv 1ury 1ut0 1v5h 2dc3 3ag0 4b3w

(-) Related Entries Specified in the PDB File

1umo THE CRYSTAL STRUCTURE OF CYTOGLOBIN: THE FOURTH GLOBIN TYPE DISCOVERED IN AMN
1urv CRYSTAL STRUCTURE OF CYTOGLOBIN: THE FOURTH GLOBIN TYPE DISCOVERED IN MAN DISPLAYS HEME HEXA-COORDINATION
1ury CYTOGLOBIN CAVITIES
1ut0 CRYSTAL STRUCTURE OF CYTOGLOBIN: THE FOURTH GLOBIN TYPE DISCOVERED IN MAN DISPLAYS HEME HEXA-COORDINATION