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(-) Description

Title :  M.ACETIVORANS PROTOGLOBIN F93Y MUTANT IN COMPLEX WITH CYANIDE
 
Authors :  L. Tilleman, S. Abbruzzetti, C. Ciaccio, G. De Sanctis, M. Nardini, A. F. Desmet, L. Moens, S. Van Doorslaer, S. Bruno, M. Bolognesi, P. Asce M. Coletta, C. Viappiani, S. Dewilde
Date :  22 Feb 13  (Deposition) - 12 Mar 14  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxygen Transport, Haem-Distal Site Mutation, Cyanide Complex, Allosteric Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Tilleman, S. Abbruzzetti, C. Ciaccio, G. De Sanctis, M. Nardini, A. Pesce, F. Desmet, L. Moens, S. Van Doorslaer, S. Bruno, M. Bolognesi, P. Ascenzi, M. Coletta, C. Viappiani, S. Dewilde
Structural Bases For The Regulation Of Co Binding In The Archaeal Protoglobin From Methanosarcina Acetivorans.
Plos One V. 10 25959 2015
PubMed-ID: 26047471  |  Reference-DOI: 10.1371/JOURNAL.PONE.0125959

(-) Compounds

Molecule 1 - PROTOGLOBIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: METHANOSARCINA ACETIVORANS
    Organism Taxid: 2214

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CYN2Ligand/IonCYANIDE ION
2GOL2Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:70 , TYR A:73 , PHE A:74 , TYR A:85 , VAL A:89 , ARG A:92 , TYR A:93 , TRP A:96 , TYR A:112 , ARG A:119 , HIS A:120 , LYS A:125 , ASN A:126 , ILE A:137 , TYR A:141 , PHE A:145 , ILE A:149 , VAL A:182 , TRP A:185 , CYN A:201 , HOH A:2107 , HOH A:2108 , HOH A:2131 , HOH A:2136BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWARETRP A:60 , TYR A:61 , TYR A:93 , HEM A:200BINDING SITE FOR RESIDUE CYN A 201
3AC3SOFTWARELEU B:70 , TYR B:73 , PHE B:74 , TYR B:85 , VAL B:89 , ARG B:92 , TYR B:93 , TRP B:96 , TYR B:112 , ARG B:119 , HIS B:120 , LYS B:125 , ASN B:126 , ILE B:137 , TYR B:141 , PHE B:145 , ILE B:149 , VAL B:182 , TRP B:185 , CYN B:201 , HOH B:2120 , HOH B:2121 , HOH B:2139 , HOH B:2143BINDING SITE FOR RESIDUE HEM B 200
4AC4SOFTWARETRP B:60 , TYR B:61 , TYR B:93 , HEM B:200BINDING SITE FOR RESIDUE CYN B 201
5AC5SOFTWARELYS A:191 , TYR A:192 , GLU B:165 , LYS B:191 , TYR B:192BINDING SITE FOR RESIDUE GOL B1196
6AC6SOFTWAREASP B:51 , GLN B:52 , VAL B:53 , GLU B:54 , GLU B:55BINDING SITE FOR RESIDUE GOL B1197
7AC7SOFTWAREHOH A:2184 , HOH A:2185 , ARG B:122 , PRO B:135 , HOH B:2092 , HOH B:2155BINDING SITE FOR RESIDUE SO4 B1198
8AC8SOFTWAREASN A:102 , SER A:104 , HOH A:2117 , ARG B:103 , SER B:104BINDING SITE FOR RESIDUE SO4 B1199

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZOL)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZOL)

(-) 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:191
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q8TLY9_METAC     5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zol A   5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRYSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q8TLY9_METAC     5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zol B   5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRYSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8TLY9_METAC | Q8TLY9)
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).

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 Related Entries

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

UniProtKB/TrEMBL
        Q8TLY9_METAC | Q8TLY9: 2veb 2vee 3qzx 3qzz 3r0g 3zh0 3zjh 3zji 3zjj 3zjl 3zjm 3zjn 3zjo 3zjp 3zjq 3zjr 3zjs 3zom

(-) Related Entries Specified in the PDB File

3zom M.ACETIVORANS PROTOGLOBIN F145W MUTANT IN COMPLEX WITH CYANIDE