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(-) Description

Title :  CRYSTAL STRUCTURE DETERMINATION OF JAPANESE QUAIL (COTURNIX COTURNIX JAPONICA) HEMOGLOBIN AT 2.76 ANGSTROM RESOLUTION
 
Authors :  M. Thenmozhi, Pon. Sathya Moorthy, M. Balasubramanian, M. N. Ponnusw
Date :  13 Apr 10  (Deposition) - 08 Dec 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.76
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Avian Hemoglobin, High Oxygen Affinity, Oxygen Binding, Oxygen Transport, Oxygen Storage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Thenmozhi, Pon. Sathya Moorthy, M. Balasubramanian, M. N. Ponnuswamy
Crystal Structure Determination Of Japanese Quail (Coturnix Coturnix Japonica) Hemoglobin At 2. 76 Angstrom Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA-A
    Cell: RBC
    Chains: A, C
    Organism Common: JAPANESE QUAIL
    Organism Scientific: COTURNIX JAPONICA
    Organism Taxid: 93934
    Synonym: HEMOGLOBIN ALPHA-A CHAIN, ALPHA-A-GLOBIN
    Tissue: BLOOD
 
Molecule 2 - HEMOGLOBIN SUBUNIT BETA
    Cell: RBC
    Chains: B, D
    Organism Common: JAPANESE QUAIL
    Organism Scientific: COTURNIX JAPONICA
    Organism Taxid: 93934
    Synonym: HEMOGLOBIN BETA CHAIN, BETA-GLOBIN
    Tissue: BLOOD

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2OXY3Ligand/IonOXYGEN MOLECULE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , PHE A:43 , HIS A:45 , PHE A:46 , LYS A:61 , LEU A:66 , LEU A:83 , LEU A:86 , HIS A:87 , VAL A:93 , ASN A:97 , LEU A:101 , LEU A:136 , OXY A:151BINDING SITE FOR RESIDUE HEM A 150
2AC2SOFTWAREHIS A:58 , VAL A:62 , HEM A:150BINDING SITE FOR RESIDUE OXY A 151
3AC3SOFTWAREPHE B:41 , PHE B:42 , LYS B:66 , SER B:70 , PHE B:71 , HIS B:92 , ASN B:102 , LEU B:141 , OXY B:151BINDING SITE FOR RESIDUE HEM B 150
4AC4SOFTWAREPHE B:42 , HIS B:63 , VAL B:67 , HEM B:150BINDING SITE FOR RESIDUE OXY B 151
5AC5SOFTWARETYR C:42 , PHE C:43 , HIS C:45 , HIS C:58 , LYS C:61 , VAL C:62 , HIS C:87 , VAL C:93 , ASN C:97 , PHE C:98 , VAL C:132 , OXY C:151BINDING SITE FOR RESIDUE HEM C 150
6AC6SOFTWAREHIS C:58 , HEM C:150BINDING SITE FOR RESIDUE OXY C 151
7AC7SOFTWAREPHE D:41 , PHE D:42 , HIS D:63 , SER D:70 , LEU D:88 , HIS D:92 , LEU D:96 , VAL D:98 , ASN D:102 , LEU D:141BINDING SITE FOR RESIDUE HEM D 150

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MJP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MJP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MJP)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_COTJA3-142
 		  2A:2-141
C:2-141
HBB_COTJA4-146
 		  2B:4-146
D:4-146

(-) Exons   (0, 0)

(no "Exon" information available for 3MJP)

(-) 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:141
 aligned with HBA_COTJA | P24589 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_COTJA     2 VLSAADKTNVKGIFAKIAGHAEEYGAEALDRMFTTYPQTKTYFPHFDVSHGSAQIKGHGKKVAAALVEAANHIDDIAGTLSKLSDLHAQKLRVDPVNFKLLGQCFLVVVAIHHPAALTPEVHASLDKFLCAVGTVLTAKYR 142
               SCOP domains d3mjpa_ A: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhh.......hhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjp A   1 VLSAADKTNVKGIFAKIAGHAEEYGAEALDRMFTTYPQTKTYFPHFDVSHGSAQIKGHGKKVAAALVEAANHIDDIAGTLSKLSDLHAQKLRVDPVNFKLLGQCFLVVVAIHHPAALTPEVHASLDKFLCAVGTVLTAKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with HBB_COTJA | P30893 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_COTJA     1 VHWSAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFTKDFTPECQAAWQKLVRVVAHALARKYH 146
               SCOP domains d3mjpb_ B: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-146 UniProt: 4-146                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjp B   1 VHWSAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFTKDFTPECQAAWQKLVRVVAHALARKYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      


Chain C from PDB  Type:PROTEIN  Length:141
 aligned with HBA_COTJA | P24589 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_COTJA     2 VLSAADKTNVKGIFAKIAGHAEEYGAEALDRMFTTYPQTKTYFPHFDVSHGSAQIKGHGKKVAAALVEAANHIDDIAGTLSKLSDLHAQKLRVDPVNFKLLGQCFLVVVAIHHPAALTPEVHASLDKFLCAVGTVLTAKYR 142
               SCOP domains d3mjpc_ C: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Globin-3mjpC01 C:6-106                                                                               ----------------------------------- Pfam domains (1)
           Pfam domains (2) -----Globin-3mjpC02 C:6-106                                                                               ----------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: C:2-141 UniProt: 3-142                                                                                                          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjp C   1 VLSAADKTNVKGIFAKIAGHAEEYGAEALDRMFTTYPQTKTYFPHFDVSHGSAQIKGHGKKVAAALVEAANHIDDIAGTLSKLSDLHAQKLRVDPVNFKLLGQCFLVVVAIHHPAALTPEVHASLDKFLCAVGTVLTAKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 


Chain D from PDB  Type:PROTEIN  Length:146
 aligned with HBB_COTJA | P30893 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_COTJA     1 VHWSAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFTKDFTPECQAAWQKLVRVVAHALARKYH 146
               SCOP domains d3mjpd_ D: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Globin-3mjpD01 D:7-111                                                                                   ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-3mjpD02 D:7-111                                                                                   ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: D:4-146 UniProt: 4-146                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjp D   1 VHWSAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFTKDFTPECQAAWQKLVRVVAHALARKYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MJP)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (HBA_COTJA | P24589)
molecular function
    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: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: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: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:0005833    hemoglobin complex    An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain B,D   (HBB_COTJA | P30893)
molecular function
    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: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: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: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:0005833    hemoglobin complex    An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

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  3mjp
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 Related Entries

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