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(-) Description

Title :  FUNCTIONAL AND STRUCTURAL ROLE OF THE N-TERMINAL EXTENSION IN METHANOSARCINA ACETIVORANS PROTOGLOBIN
 
Authors :  C. Ciaccio, A. Pesce, G. R. Tundo, L. Tilleman, S. Dewilde, L. Moens, P. A M. Bolognesi, M. Nardini, M. Coletta
Date :  19 Dec 12  (Deposition) - 27 Mar 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Oxygen Transport, Spectroscopic Properties, Ligand Binding Properties, N-Terminal Trimming. (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Ciaccio, A. Pesce, G. R. Tundo, L. Tilleman, L. Bertolacci, S. Dewilde, L. Moens, P. Ascenzi, M. Bolognesi, M. Nardini, M. Coletta
Functional And Structural Role Of The N-Terminal Extension In Methanosarcina Acetivorans Protoglobin.
Biochim. Biophys. Acta V. 1834 1813 2013
PubMed-ID: 23485914  |  Reference-DOI: 10.1016/J.BBAPAP.2013.02.026

(-) Compounds

Molecule 1 - PROTOGLOBIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 21-195
    MutationYES
    Organism ScientificMETHANOSARCINA ACETIVORANS C2A
    Organism Taxid188937
    Other DetailsTRUNCATED FORM (WITHOUT THE FIRST 20 N-TERMINAL RESIDUES)

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2GOL8Ligand/IonGLYCEROL
3HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL3Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL5Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU 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:146 , ILE A:149 , VAL A:182 , TRP A:185 , FMT A:201 , HOH A:2064 , HOH A:2065 , HOH A:2099 , HOH A:2101BINDING SITE FOR RESIDUE HEM A 200
02AC2SOFTWARETRP A:60 , TYR A:61 , PHE A:93 , HEM A:200BINDING SITE FOR RESIDUE FMT A 201
03AC3SOFTWARELEU 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 , LYS B:125 , ASN B:126 , ILE B:137 , TYR B:141 , LEU B:142 , PHE B:145 , ILE B:146 , ILE B:149 , VAL B:182 , TRP B:185 , FMT B:201 , HOH B:2063 , HOH B:2064 , HOH B:2088 , HOH B:2092BINDING SITE FOR RESIDUE HEM B 200
04AC4SOFTWARETRP B:60 , TYR B:61 , PHE B:93 , HEM B:200BINDING SITE FOR RESIDUE FMT B 201
05AC5SOFTWARELEU C:70 , TYR C:73 , PHE C:74 , TYR C:85 , VAL C:89 , ARG C:92 , PHE C:93 , TRP C:96 , TYR C:112 , ARG C:119 , HIS C:120 , LYS C:125 , ASN C:126 , ILE C:137 , TYR C:141 , LEU C:142 , PHE C:145 , ILE C:146 , ILE C:149 , VAL C:182 , TRP C:185 , FMT C:201 , HOH C:2061 , HOH C:2062 , HOH C:2088 , HOH C:2093BINDING SITE FOR RESIDUE HEM C 200
06AC6SOFTWARETRP C:60 , TYR C:61 , PHE C:93 , HEM C:200BINDING SITE FOR RESIDUE FMT C 201
07AC7SOFTWARELEU D:70 , TYR D:73 , PHE D:74 , TYR D:85 , VAL D:89 , ARG D:92 , PHE D:93 , TRP D:96 , TYR D:112 , ARG D:119 , HIS D:120 , LYS D:125 , ASN D:126 , ILE D:137 , TYR D:141 , LEU D:142 , PHE D:145 , ILE D:149 , VAL D:182 , TRP D:185 , FMT D:201 , HOH D:2071 , HOH D:2072 , HOH D:2096 , HOH D:2098BINDING SITE FOR RESIDUE HEM D 200
08AC8SOFTWARETRP D:60 , TYR D:61 , PHE D:93 , HEM D:200BINDING SITE FOR RESIDUE FMT D 201
09AC9SOFTWAREGLN A:52 , VAL A:53 , GLU A:54 , GLU A:55BINDING SITE FOR RESIDUE GOL A1196
10BC1SOFTWAREMET C:20 , TYR C:114 , LEU C:184 , TYR C:187 , HOH C:2001 , HOH C:2124BINDING SITE FOR RESIDUE GOL C1196
11BC2SOFTWARESER C:76 , PRO C:77 , ASP C:78 , THR C:80 , HOH C:2046BINDING SITE FOR RESIDUE GOL C1197
12BC3SOFTWAREASP C:111 , TYR C:114BINDING SITE FOR RESIDUE GOL C1198
13BC4SOFTWAREGLU A:47 , ALA D:108 , ASP D:111 , TYR D:112 , HOH D:2084BINDING SITE FOR RESIDUE GOL D1196
14BC5SOFTWAREMET B:20 , ASP B:111 , HOH B:2001BINDING SITE FOR RESIDUE GOL B1196
15BC6SOFTWAREASN C:126 , VAL C:131 , GLU C:132 , SER C:133 , HOH C:2081 , HOH C:2095 , HOH C:2097BINDING SITE FOR RESIDUE GOL C1199
16BC7SOFTWARELYS A:26 , LYS A:29 , PHE A:34 , THR A:35 , ALA A:36 , GLU A:39BINDING SITE FOR RESIDUE GOL A1197

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZH0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZH0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZH0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZH0)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZH0)

(-) 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:176
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:176
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      
         Q8TLY9_METAC    20 FNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zh0 A  20 MNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:176
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      
         Q8TLY9_METAC    20 FNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zh0 B  20 MNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      

Chain C from PDB  Type:PROTEIN  Length:176
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:176
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      
         Q8TLY9_METAC    20 FNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 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
                 3zh0 C  20 MNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      

Chain D from PDB  Type:PROTEIN  Length:176
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:176
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      
         Q8TLY9_METAC    20 FNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 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
                 3zh0 D  20 MNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3ZH0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZH0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZH0)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 | Q8TLY92veb 2vee 3qzx 3qzz 3r0g 3zjh 3zji 3zjj 3zjl 3zjm 3zjn 3zjo 3zjp 3zjq 3zjr 3zjs 3zol 3zom

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3ZH0)