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(-) Description

Title :  Y29A MUTANT OF VITREOSCILLA STERCORARIA HEMOGLOBIN
 
Authors :  S. Ratakonda, A. Anand, K. Dikshit, B. C. Stark, A. J. Howard
Date :  31 Aug 11  (Deposition) - 16 Apr 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Globin 8-Helix Fold, Oxygen Storage, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ratakonda, A. Anand, K. Dikshit, B. C. Stark, A. J. Howard
Crystallographic Structure Determination Of B10 Mutants Of Vitreoscilla Hemoglobin: Role Of Tyr29 (B10) In The Structure Of The Ligand-Binding Site.
Acta Crystallogr. , Sect. F V. 69 215 2013
PubMed-ID: 23519792  |  Reference-DOI: 10.1107/S1744309112044818

(-) Compounds

Molecule 1 - BACTERIAL HEMOGLOBIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDH88
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 668369
    Expression System Vector Type: PLASMID
    Gene: VHB
    Mutation: YES
    Organism Scientific: VITREOSCILLA STERCORARIA
    Organism Taxid: 61
    Synonym: SOLUBLE CYTOCHROME O

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 26)
No.NameCountTypeFull Name
1EDO24Ligand/Ion1,2-ETHANEDIOL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:42 , PHE A:43 , GLN A:53 , ALA A:56 , LEU A:57 , THR A:60 , ILE A:81 , LYS A:84 , HIS A:85 , TYR A:95 , VAL A:98 , TYR A:126 , PHE A:133 , HOH A:311 , HOH A:407 , HOH A:409BINDING SITE FOR RESIDUE HEM A 201
02AC2SOFTWARELYS A:107 , THR A:115 , ASP A:116 , EDO A:207 , HOH A:348 , HOH A:352 , HOH A:373BINDING SITE FOR RESIDUE EDO A 203
03AC3SOFTWARETHR A:23 , THR A:27 , LYS A:30 , VAL A:145BINDING SITE FOR RESIDUE EDO A 204
04AC4SOFTWAREGLN A:4 , GLN A:5 , HOH A:366BINDING SITE FOR RESIDUE EDO A 205
05AC5SOFTWARELYS A:79 , HOH A:389BINDING SITE FOR RESIDUE EDO A 206
06AC6SOFTWARETHR A:27 , LYS A:107 , GLU A:108 , GLY A:111 , ASP A:112 , EDO A:203 , HOH A:364BINDING SITE FOR RESIDUE EDO A 207
07AC7SOFTWAREPRO A:76 , LYS A:79 , HOH A:305 , HOH A:378BINDING SITE FOR RESIDUE EDO A 209
08AC8SOFTWAREGLY A:127 , ASP A:131 , EDO A:212 , HOH A:387BINDING SITE FOR RESIDUE EDO A 210
09AC9SOFTWAREMET A:1 , GLN A:135BINDING SITE FOR RESIDUE EDO A 211
10BC1SOFTWARETYR A:95 , GLY A:127 , ASP A:131 , EDO A:210 , HOH A:377BINDING SITE FOR RESIDUE EDO A 212
11BC2SOFTWAREHOH A:337BINDING SITE FOR RESIDUE EDO A 213

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TM9)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.BAHG_VITST1-135  1A:1-135
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.BAHG_VITST1-135  2A:1-135

(-) Exons   (0, 0)

(no "Exon" information available for 3TM9)

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

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           BAHG_VITST     1 MLDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLFDMGRQESLEQPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAVE 146
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GLOBIN  PDB: A:1-135 UniProt: 1-135                                                                                                    ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tm9 A   1 MLDQQTINIIKATVPVLKEHGVTITTTFAKNLFAKHPEVRPLFDMGRQESLEQPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAVE 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3TM9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TM9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TM9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (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: 1vhb 2vhb 3tld 3tm3 3vhb 4vhb

(-) Related Entries Specified in the PDB File

2vhb THE WILD-TYPE VITREOSCILLA HEMOGLOBIN STRUCTURE COMPLEXED WITH AZIDE, AS DETERMINED BY TARRICONE ET AL.
3tld Y29F MUTANT OF THIS PROTEIN
3tm3 WILD-TYPE VITREOSCILLA HEMOGLOBIN, AS DETERMINED HERE