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(-) Description

Title :  CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II GENERATED AFTER ANNEALING OF PEROXYMYOGLOBIN
 
Authors :  H. -P. Hersleth, C. H. Gorbitz, K. K. Andersson
Date :  20 Jan 08  (Deposition) - 29 Jan 08  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Haem, Iron, Heme, Ferryl, Transport, Peroxidase, Oxygen Transport, Oxygen Activation, Radiolytic- Reduction, Reaction Intermediate, Monooxygenase, Metal-Binding, Muscle Protein, X-Ray-Induced-Photoreduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -P. Hersleth, Y. Hsiao, U. Ryde, C. H. Gorbitz, K. K. Andersson
The Crystal Structure Of Peroxymyoglobin Generated Through Cryoradiolytic Reduction Of Myoglobin Compound Iii During Data Collection.
Biochem. J. V. 412 257 2008
PubMed-ID: 18215120  |  Reference-DOI: 10.1042/BJ20070921
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYOGLOBIN
    Chains: A
    Fragment: RESIDUES 2-154
    Organ: HEART
    Organism Common: HORSE
    Organism Scientific: EQUUS CABALLUS
    Organism Taxid: 9796
    Other Details: FE(IV)OH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OH1Ligand/IonHYDROXIDE ION
4PEO3Ligand/IonHYDROGEN PEROXIDE
5SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:39 , LYS A:42 , PHE A:43 , LYS A:45 , VAL A:68 , LEU A:89 , SER A:92 , HIS A:93 , HIS A:97 , ILE A:99 , TYR A:103 , LEU A:104 , HIS A:113 , HIS A:116 , GLN A:128 , PHE A:138 , OH A:1155 , HOH A:2145 , HOH A:2146 , HOH A:2147 , HOH A:2148 , HOH A:2149 , HOH A:2150BINDING SITE FOR RESIDUE HEM A1154
2AC2SOFTWAREHIS A:64 , VAL A:68 , HEM A:1154BINDING SITE FOR RESIDUE OH A1155
3AC3SOFTWARETHR A:51 , GLU A:52 , HOH A:2065 , HOH A:2152BINDING SITE FOR RESIDUE SO4 A1156
4AC4SOFTWAREGLY A:1 , HOH A:2153 , HOH A:2154 , HOH A:2155BINDING SITE FOR RESIDUE SO4 A1157
5AC5SOFTWAREARG A:31 , HIS A:36 , LYS A:96 , ASP A:109 , ALA A:110 , HOH A:2156 , HOH A:2157 , HOH A:2158 , HOH A:2159BINDING SITE FOR RESIDUE GOL A1158
6AC6SOFTWAREGLY A:1 , LEU A:2 , TRP A:7BINDING SITE FOR RESIDUE PEO A1159
7AC7SOFTWAREGLU A:59 , LYS A:62 , LYS A:63BINDING SITE FOR RESIDUE PEO A1160
8AC8SOFTWARELYS A:16 , HIS A:24 , HIS A:119BINDING SITE FOR RESIDUE PEO A1161

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VM0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VM0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VM0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.MYG_HORSE3-148  1A:2-147

(-) Exons   (0, 0)

(no "Exon" information available for 2VM0)

(-) 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:153
 aligned with MYG_HORSE | P68082 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
            MYG_HORSE     2 GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG 154
               SCOP domains d2vm0a_ A: Myoglobin                                                                                                                                      SCOP domains
               CATH domains 2vm0A00 A:1-153 Globins                                                                                                                                   CATH domains
               Pfam domains -----Globin-2vm0A01 A:6-112                                                                                     ----------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-147 UniProt: 3-148                                                                                                               ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vm0 A   1 GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MYG_HORSE | P68082)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0050873    brown fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
    GO:0043353    enucleate erythrocyte differentiation    The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    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: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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MYG_HORSE | P68082: 1azi 1bje 1dwr 1dws 1dwt 1gjn 1hrm 1hsy 1npf 1npg 1nz2 1nz3 1nz4 1nz5 1rse 1wla 1xch 1yma 1ymb 1ymc 2frf 2fri 2frj 2frk 2in4 2nsr 2nss 2o58 2o5b 2o5l 2o5m 2o5o 2o5q 2o5s 2o5t 2v1e 2v1f 2v1g 2v1h 2v1i 2v1j 2v1k 2vlx 2vly 2vlz 3ba2 3hc9 3hen 3heo 3hep 3lr7 3lr9 3rj6 3rjn 3v2v 3v2z 3vau 3vm9 3wft 3wfu 3wi8 3wyo 4dc7 4dc8 4ns2 4twu 4twv 5azq 5azr 5cmv 5cn4 5cn5 5cn6 5cn7 5cn8 5cn9 5cnb 5cnc 5cnd 5cne 5cnf 5cng 5d5r

(-) Related Entries Specified in the PDB File

1azi MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE COMPLEXED WITH AZIDE
1bje H64T VARIANT OF MYOGLOBIN (HORSE HEART) RECOMBINANT WILD- TYPE COMPLEXED WITH AZIDE
1dwr MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH CO
1dws MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH CO
1dwt PHOTORELAXED HORSE HEART MYOGLOBIN CO COMPLEX
1gjn HYDROGEN PEROXIDE DERIVED MYOGLOBIN COMPOUND II AT PH 5.2
1hrm MYOGLOBIN MUTANT WITH HIS 93 REPLACED BY TYR (H93Y)
1hsy MYOGLOBIN MUTANT WITH HIS 64 REPLACED BY THR (H64T)
1npf MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITRICOXIDE
1npg MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITHNITROSOETHANE
1nz2 K45E VARIANT OF HORSE HEART MYOGLOBIN
1nz3 K45E-K63E VARIANT OF HORSE HEART MYOGLOBIN
1nz4 THE HORSE HEART MYOGLOBIN VARIANT K45E/K63E COMPLEXED WITHCADMIUM
1nz5 THE HORSE HEART MYOGLOBIN VARIANT K45E/K63E COMPLEXED WITHMANGANESE
1rse MYOGLOBIN (HORSE HEART) MUTANT WITH SER 92 REPLACED BY ASP (S92D)
1wla MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE
1xch MYOGLOBIN (HORSE HEART) MUTANT WITH LEU 104 REPLACED BY ASN (L104N)
1yma MYOGLOBIN (HORSE HEART) MUTANT WITH HIS 64 REPLACED BY TYR (H64Y)
1ymb METMYOGLOBIN (HORSE HEART)
1ymc CYANOMET-SULFMYOGLOBIN (HORSE HEART)
2frf HORSE HEART MYOGLOBIN, NITRITE ADDUCT, CRYSTAL SOAK
2fri HORSE HEART MYOGLOBIN, NITRITE ADDUCT, CO- CRYSTALLIZED
2frj NITROSYL HORSE HEART MYOGLOBIN, NITRITE/ DITHIONITE METHOD
2frk NITROSYL HORSE HEART MYOGLOBIN, NITRIC OXIDE GAS METHOD
2in4 CRYSTAL STRUCTURE OF MYOGLOBIN WITH CHARGE NEUTRALIZED HEME, ZNDMB-DME
2v1e CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II - INTERMEDIATE H AT PH 6.8
2v1f CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II - INTERMEDIATE H AT PH 8.7
2v1g CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II - INTERMEDIATE H AT PH 5.2
2v1h CRYSTAL STRUCTURE OF RADIATION-INDUCED METMYOGLOBIN - AQUA FERROUS MYOGLOBIN AT PH 5.2
2v1i CRYSTAL STRUCTURE OF RADIATION-INDUCED METMYOGLOBIN - AQUA FERROUS MYOGLOBIN AT PH 6.8
2v1j CRYSTAL STRUCTURE OF RADIATION-INDUCED METMYOGLOBIN - AQUA FERROUS MYOGLOBIN AT PH 8.7
2v1k CRYSTAL STRUCTURE OF FERROUS DEOXYMYOGLOBIN AT PH 6.8
2vlx CRYSTAL STRUCTURE OF PEROXYMYOGLOBIN GENERATED BY CRYORADIOLYTIC REDUCTION OF MYOGLOBIN COMPOUND III
2vly CRYSTAL STRUCTURE OF MYOGLOBIN COMPOUND III ( RADIATION- INDUCED)
2vlz CRYSTAL STRUCTURE OF PEROXYMYOGLOBIN GENERATED BY CRYORADIOLYTIC REDUCTION OF MYOGLOBIN COMPOUND III