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(-) Description

Title :  R/T INTERMEDIATE QUATERNARY STRUCTURE OF AN ANTARCTIC FISH HEMOGLOBIN IN AN ALPHA(CO)-BETA(PENTACOORDINATE) STATE
 
Authors :  L. Vitagliano, A. Vergara, G. Bonomi, A. Merlino, L. Mazzarella
Date :  06 May 08  (Deposition) - 05 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Antarctic Fish Hemoglobin, Intermediate R/T Quaternary Structure, Oxidation Pathway, Heme, Iron, Metal-Binding, Oxygen Transport, Transport, Acetylation, Oxygen Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Vitagliano, A. Vergara, G. Bonomi, A. Merlino, C. Verde, G. Di Prisco, B. D. Howes, G. Smulevich, L. Mazzarella
Spectroscopic And Crystallographic Characterization Of A Tetrameric Hemoglobin Oxidation Reveals Structural Features Of The Functional Intermediate Relaxed/Tense State.
J. Am. Chem. Soc. V. 130 10527 2008
PubMed-ID: 18642904  |  Reference-DOI: 10.1021/JA803363P
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA-1
    Chains: A
    Organism Common: DUSKY NOTOTHEN
    Organism Taxid: 35730
    Other Details: GENE HBA1
    Synonym: HEMOGLOBIN ALPHA-1 CHAIN, ALPHA-1-GLOBIN
 
Molecule 2 - HEMOGLOBIN SUBUNIT BETA-1/2
    Chains: B
    Organism Common: DUSKY NOTOTHEN
    Organism Taxid: 35730
    Synonym: HEMOGLOBIN BETA-1/2 CHAIN, BETA-1/2-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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CMO1Ligand/IonCARBON MONOXIDE
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CMO2Ligand/IonCARBON MONOXIDE
3HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:1 , LEU A:2 , LEU A:135BINDING SITE FOR RESIDUE ACE A 0
2AC2SOFTWARELEU A:29 , HIS A:59BINDING SITE FOR RESIDUE CMO A 199
3AC3SOFTWARETYR A:42 , HIS A:45 , TRP A:46 , HIS A:59 , LYS A:62 , LEU A:84 , GLN A:87 , HIS A:88 , LEU A:92 , ASN A:98 , LEU A:102 , ASN A:103 , LEU A:137BINDING SITE FOR RESIDUE HEM A 200
4AC4SOFTWARETHR B:38 , TYR B:41 , PHE B:42 , PHE B:45 , HIS B:63 , LEU B:91 , HIS B:92 , LEU B:96 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141BINDING SITE FOR RESIDUE HEM B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D1K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D1K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D1K)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA1_TRENE2-142  1A:2-142
HBB_TRENE4-146  1B:4-146
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA1_TRENE2-142  2A:2-142
HBB_TRENE4-146  2B:4-146

(-) Exons   (0, 0)

(no "Exon" information available for 3D1K)

(-) 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 HBA1_TRENE | P45718 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:143
                                                                                                                                                                       142 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 | 
           HBA1_TRENE     1 SLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR-   -
               SCOP domains d3d1ka_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains 3d1kA00 A:1-142 Globins                                                                                                                       - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-142 UniProt: 2-142                                                                                                          - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d1k A   1 SLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYRx   0
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 ||
                                                                                                                                                                       142|
                                                                                                                                                                          0-ACE


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with HBB_TRENE | P45720 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_TRENE     1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLVVYPWTQRYFSGFGNLYNAEGIMSNANVAAHGIKVLHGLDRGMKNMDNIADAYTDLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAAVVSALGKQYH 146
               SCOP domains d3d1kb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 3d1kB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-146 UniProt: 4-146                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d1k B   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLVVYPWTQRYFSGFGNLYNAEGIMSNANVAAHGIKVLHGLDRGMKNMDNIADAYTDLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAAVVSALGKQYH 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  (2, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D1K)

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (HBA1_TRENE | P45718)
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_TRENE | P45720)
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
        HBA1_TRENE | P45718: 1la6 1t1n 2aa1 3nfe 3ng6
        HBB_TRENE | P45720: 1la6 1t1n 3nfe 3ng6

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