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(-) Description

Title :  CRYSTAL STRUCTURE OF TREMATOMUS BERNACCHII HEMOGLOBIN IN A PARTIAL HEMICHROME STATE
 
Authors :  A. Vergara, M. Franzese, A. Merlino, L. Vitagliano, L. Mazzarella
Date :  03 Apr 07  (Deposition) - 24 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hemichrome, R/Tintermediate Quaternary Structure, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Vergara, M. Franzese, A. Merlino, L. Vitagliano, C. Verde, G. Di Prisco, H. C. Lee, J. Peisach, L. Mazzarella
Structural Characterization Of Ferric Hemoglobins From Three Antarctic Fish Species Of The Suborder Notothenioidei.
Biophys. J. V. 93 2822 2007
PubMed-ID: 17545238  |  Reference-DOI: 10.1529/BIOPHYSJ.107.105700
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA
    Chains: A
    Organism Common: EMERALD ROCKCOD
    Organism Scientific: TREMATOMUS BERNACCHII
    Organism Taxid: 40690
    Synonym: HEMOGLOBIN ALPHA CHAIN, ALPHA-GLOBIN
 
Molecule 2 - HEMOGLOBIN SUBUNIT BETA
    Chains: B
    Organism Common: EMERALD ROCKCOD
    Organism Scientific: TREMATOMUS BERNACCHII
    Organism Taxid: 40690
    Synonym: HEMOGLOBIN BETA CHAIN, BETA-GLOBIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , PHE A:43 , HIS A:45 , TRP A:46 , HIS A:59 , LYS A:62 , VAL A:63 , GLN A:87 , HIS A:88 , LEU A:92 , VAL A:94 , ASN A:98 , LEU A:102 , LEU A:137 , HOH A:1072BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWAREHIS B:41 , PHE B:42 , HIS B:63 , LYS B:66 , VAL B:67 , LEU B:91 , HIS B:92 , LEU B:96 , PHE B:103 , LEU B:141 , HOH B:1054BINDING SITE FOR RESIDUE HEM B 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_TREBE2-142  1A:2-142
HBB_TREBE5-147  1B:4-146
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_TREBE2-142  2A:2-142
HBB_TREBE5-147  2B:4-146

(-) Exons   (0, 0)

(no "Exon" information available for 2PEG)

(-) 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:143
 aligned with HBA_TREBE | P80043 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:143
                             1                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139   
            HBA_TREBE     - -SLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
               SCOP domains d2pega_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -2pegA00 A:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ------Globin-2pegA01 A:6-107                                                                                ----------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:2-142 UniProt: 2-142                                                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2peg A   0 xSLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            |                                                                                                                                              
                            0-ACE                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:141
 aligned with HBB_TREBE | P80044 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
            HBB_TREBE     2 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLYNAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQYH 147
               SCOP domains d2pegb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 2pegB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains ------Globin-2pegB01 B:7-111                                                                                   ----------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.-----hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-146 UniProt: 5-147                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2peg B   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSG-----NAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQYH 146
                                    10        20        30        40   |    50        60        70        80        90       100       110       120       130       140      
                                                                      44    50
   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  (2, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (HBA_TREBE | P80043)
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   (HBB_TREBE | P80044)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        HBA_TREBE | P80043: 1hbh 1pbx 1s5x 1s5y 2h8d 2h8f 3gkv 3gqg 4g51 4iro 4odc
        HBB_TREBE | P80044: 1hbh 1pbx 1s5x 1s5y 2h8d 2h8f 3gkv 3gqg 4g51 4iro 4odc

(-) Related Entries Specified in the PDB File

1la6 CRYSTAL STRUCTURE OF TETRAMERIC HEMOGLOBIN IN A PARTIAL HEMICHROME STATE
1s5x CRYSTAL STRUCTURE OF TREMATOMUS BERNACCHII HEMOGLOBIN OXIDIZED BY AIR
1s5y CRYSTAL STRUCTURE OF TREMATOMUS BERNACCHII HEMOGLOBIN OXIDIZED BY FERRICYANIDE