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(-) Description

Title :  BACTERIAL DIMERIC HEMOGLOBIN FROM VITREOSCILLA STERCORARIA
 
Authors :  C. Tarricone, A. Galizzi, A. Coda, P. Ascenzi, M. Bolognesi
Date :  19 Feb 97  (Deposition) - 25 Feb 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heme, Respiratory Protein, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Tarricone, A. Galizzi, A. Coda, P. Ascenzi, M. Bolognesi
Unusual Structure Of The Oxygen-Binding Site In The Dimeric Bacterial Hemoglobin From Vitreoscilla Sp.
Structure V. 5 497 1997
PubMed-ID: 9115439  |  Reference-DOI: 10.1016/S0969-2126(97)00206-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN
    Atcc: 15218
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: VGB
    Expression System Plasmid: PDH88
    Expression System Strain: DH5-ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: BACTERIAL
    Gene: VGB
    Organism Scientific: VITREOSCILLA STERCORARIA
    Organism Taxid: 61
    Strain: C1
    Synonym: SOLUBLE CYTOCHROME O

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:42 , PHE A:43 , PRO A:54 , LEU A:57 , THR A:60 , VAL A:61 , LYS A:84 , HIS A:85 , VAL A:90 , HIS A:94 , TYR A:95 , VAL A:98 , PHE A:133 , HOH A:166 , HOH A:198BINDING SITE FOR RESIDUE HEM A 150
2AC2SOFTWARELEU B:42 , PHE B:43 , PRO B:54 , LEU B:57 , THR B:60 , VAL B:61 , LYS B:84 , HIS B:85 , VAL B:90 , HIS B:94 , TYR B:95 , VAL B:98 , HOH B:180 , HOH B:198BINDING SITE FOR RESIDUE HEM B 150

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VHB)

(-) Exons   (0, 0)

(no "Exon" information available for 1VHB)

(-) 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:135
 aligned with BAHG_VITST | P04252 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
           BAHG_VITST     2 LDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLFDMGRQESLEQPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAV 145
               SCOP domains d1vhba_ A: Bacterial dimeric hemoglobin                                                                                                          SCOP domains
               CATH domains 1vhbA00 A:2-145 Globins                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.---------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vhb A   2 LDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLF---------QPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAV 145
                                    11        21        31        41 |       - |      61        71        81        91       101       111       121       131       141    
                                                                    43        53                                                                                            


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with BAHG_VITST | P04252 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
           BAHG_VITST     2 LDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLFDMGRQESLEQPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAV 145
               SCOP domains d1vhbb_ B: Bacterial dimeric hemoglobin                                                                                                          SCOP domains
               CATH domains 1vhbB00 B:2-145 Globins                                                                                                                          CATH domains
           Pfam domains (1) ----Globin-1vhbB01 B:6-103                                                                            ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----Globin-1vhbB02 B:6-103                                                                            ------------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.---------....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vhb B   2 LDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLF---------QPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAV 145
                                    11        21        31        41 |       - |      61        71        81        91       101       111       121       131       141    
                                                                    43        53
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BAHG_VITST | P04252)
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BAHG_VITST | P04252: 2vhb 3tld 3tm3 3tm9 3vhb 4vhb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VHB)