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(-) Description

Title :  3D STRUCTURE OF FERRIC METHANOSARCINA ACETIVORANS PROTOGLOBIN Y61A MUTANT WITH UNKNOWN LIGAND
 
Authors :  A. Pesce, L. Tilleman, S. Dewilde, P. Ascenzi, M. Coletta, C. Ciaccio, S L. Moens, M. Bolognesi, M. Nardini
Date :  07 Mar 11  (Deposition) - 08 Jun 11  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Globin Fold, Protoglobin, Methanogenesis, Archaea Protein, Oxygen Binding, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Pesce, L. Tilleman, S. Dewilde, P. Ascenzi, M. Coletta, C. Ciaccio, S. Bruno, L. Moens, M. Bolognesi, M. Nardini
Structural Heterogeneity And Ligand Gating In Ferric Methanosarcina Acetivorans Protoglobin Mutants.
Iubmb Life V. 63 287 2011
PubMed-ID: 21618401  |  Reference-DOI: 10.1002/IUB.484
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHANOSARCINA ACETIVORANS PROTOGLOBIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MA_2883
    Mutation: YES
    Organism Scientific: METHANOSARCINA ACETIVORANS
    Organism Taxid: 2214

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:70 , TYR A:73 , PHE A:74 , TYR A:85 , VAL A:89 , ARG A:92 , PHE 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 , LEU A:142 , PHE A:145 , ILE A:149 , VAL A:182 , TRP A:185 , HOH A:269 , HOH A:279 , HOH A:281 , HOH A:282BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWAREGLY A:12 , GLU A:13 , THR A:14 , GLU A:15 , ASN A:16 , ALA A:108 , ASP A:111 , HOH A:259BINDING SITE FOR RESIDUE PO4 A 201
3AC3SOFTWARETYR A:72 , VAL A:134 , PRO A:135 , ASN A:136 , HOH A:219 , HOH A:234 , HOH A:271 , HOH A:289 , HOH A:387BINDING SITE FOR RESIDUE PO4 A 202
4AC4SOFTWARETHR A:163 , PRO A:164 , GLU A:165 , TYR A:187 , PRO A:188 , VAL A:190 , LYS A:191 , TYR A:192 , HOH A:365 , HOH A:427BINDING SITE FOR RESIDUE GOL A 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QZX)

(-) 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    
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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:190
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:190
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
         Q8TLY9_METAC     6 IPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Protoglobin-3qzxA01 A:6-195                                                                                                                                                                    Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qzx A   6 IPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWAGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
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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 3QZX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Protoglobin] (5)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 3qzz 3r0g 3zh0 3zjh 3zji 3zjj 3zjl 3zjm 3zjn 3zjo 3zjp 3zjq 3zjr 3zjs 3zol 3zom

(-) Related Entries Specified in the PDB File

2veb HIGH RESOLUTION STRUCTURE OF PROTOGLOBIN FROM METHANOSARCINA ACETIVORANS C2A
2vee STRUCTURE OF FERRIC PROTOGLOBIN FROM METHANOSARCINA ACETIVORANS C2A
3qzz STRUCTURE OF FERRIC METHANOSARCINA ACETIVORANS PROTOGLOBIN Y61W MUTANT IN AQUOMET FORM
3r0g STRUCTURE OF FERRIC METHANOSARCINA ACETIVORANS PROTOGLOBIN I149F MUTANT IN AQUOMET FORM