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(-) Description

Title :  3D STRUCTURE OF FERRIC METHANOSARCINA ACETIVORANS PROTOGLOBIN I149F MUTANT IN AQUOMET FORM
 
Authors :  A. Pesce, L. Tilleman, S. Dewilde, P. Ascenzi, M. Coletta, C. Ciaccio, S L. Moens, M. Bolognesi, M. Nardini
Date :  08 Mar 11  (Deposition) - 08 Jun 11  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protoglobin, Globin Fold, 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, B
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL3Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IPA1Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
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 , TYR A:141 , PHE A:145 , ILE A:146 , TRP A:185 , HOH A:197 , HOH A:205 , HOH A:209 , HOH A:219 , HOH A:243BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWAREHOH A:218BINDING SITE FOR RESIDUE GOL A 3546
3AC3SOFTWARELYS A:191 , ASP A:194 , HIS B:121 , ARG B:122 , HOH B:222BINDING SITE FOR RESIDUE GOL A 3547
4AC4SOFTWARELEU A:27 , GLU A:30 , PRO B:68 , HIS B:69BINDING SITE FOR RESIDUE GOL A 3548
5AC5SOFTWAREPRO A:19 , ASP A:24 , ARG B:140BINDING SITE FOR RESIDUE IPA A 4571
6AC6SOFTWARELEU B:70 , TYR B:73 , PHE B:74 , TYR B:85 , VAL B:89 , ARG B:92 , PHE B:93 , TRP B:96 , TYR B:112 , ARG B:119 , HIS B:120 , ASN B:126 , ILE B:137 , TYR B:141 , PHE B:145 , ILE B:146 , TRP B:185 , HOH B:198 , HOH B:212 , HOH B:216 , HOH B:240BINDING SITE FOR RESIDUE HEM B 200
7AC7SOFTWAREHIS A:121 , ARG A:122 , THR A:123 , GLY A:161 , HIS A:162 , THR A:163 , HOH A:272 , LYS B:191 , TYR B:192 , ASP B:194BINDING SITE FOR RESIDUE EPE B 3380

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R0G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R0G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R0G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R0G)

(-) Exons   (0, 0)

(no "Exon" information available for 3R0G)

(-) 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.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r0g A   5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPFTATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 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 (1) Protoglobin-3r0gB01 B:5-195                                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) Protoglobin-3r0gB02 B:5-195                                                                                                                                                                     Pfam domains (2)
         Sec.struct. author ................hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r0g B   5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPFTATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 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 3R0G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R0G)

(-) Pfam Domains  (1, 2)

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

(-) 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 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
3qzx STRUCTURE OF FERRIC METHANOSARCINA ACETIVORANS PROTOGLOBIN Y61A MUTANT WITH UNKNOWN LIGAND
3qzz STRUCTURE OF FERRIC METHANOSARCINA ACETIVORANS PROTOGLOBIN Y61W MUTANT IN AQUOMET FORM