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(-) Description

Title :  CRYSTAL STRUCTURE OF Y29F MUTANT OF VITREOSCILLA HEMOGLOBIN
 
Authors :  S. Ratakonda, A. Anand, K. Dikshit, B. C. Stark, A. J. Howard
Date :  29 Aug 11  (Deposition) - 16 Apr 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
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, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PY29F
    Expression System Strain: PET-28C
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VHB
    Mutation: YES
    Organism Scientific: VITREOSCILLA STERCORARIA
    Organism Taxid: 61
    Synonym: SOLUBLE CYTOCHROME O

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:42 , PHE A:43 , PRO A:54 , LEU A:57 , THR A:60 , VAL A:61 , ILE A:81 , LYS A:84 , HIS A:85 , VAL A:90 , HIS A:94 , TYR A:95 , VAL A:98 , PHE A:133 , HOH A:302 , HOH A:321 , HOH A:330 , HOH A:392 , HOH A:414BINDING SITE FOR RESIDUE HEM A 201
2AC2SOFTWAREASP A:112 , HOH A:405 , HOH A:415BINDING SITE FOR RESIDUE GOL A 202
3AC3SOFTWARELEU B:42 , PHE B:43 , PRO B:54 , LEU B:57 , THR B:60 , VAL B:61 , ILE B:81 , LYS B:84 , HIS B:85 , VAL B:90 , HIS B:94 , TYR B:95 , VAL B:98 , TYR B:126 , HOH B:327 , HOH B:334 , HOH B:340 , HOH B:381BINDING SITE FOR RESIDUE HEM B 201
4AC4SOFTWAREHOH B:400BINDING SITE FOR RESIDUE GOL B 202
5AC5SOFTWAREPRO A:76 , ASP B:139 , GLN B:143 , HOH B:407BINDING SITE FOR RESIDUE GOL B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TLD)

(-) 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    
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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:144
 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 ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GLOBIN  PDB: A:1-135 UniProt: 1-135                                                                                                    ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tld A   1 MLDQQTINIIKATVPVLKEHGVTITTTFFKNLFAKHPEVRPLFDMG--ESLEQPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAVE 146
                                    10        20        30        40     |  50        60        70        80        90       100       110       120       130       140      
                                                                        46 49                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:144
 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 ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--.......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GLOBIN  PDB: B:1-135 UniProt: 1-135                                                                                                    ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tld B   1 MLDQQTINIIKATVPVLKEHGVTITTTFFKNLFAKHPEVRPLFDMG--ESLEQPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAVE 146
                                    10        20        30        40     |  50        60        70        80        90       100       110       120       130       140      
                                                                        46 49
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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 3TLD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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: 1vhb 2vhb 3tm3 3tm9 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.
3tm3
3tm9