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(-) Description

Title :  PHE(93)E11LEU MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
 
Authors :  A. Pesce, L. Tilleman, J. Donne, E. Aste, P. Ascenzi, C. Ciaccio, M. Cole L. Moens, C. Viappiani, S. Dewilde, M. Bolognesi, M. Nardini
Date :  18 Jan 13  (Deposition) - 26 Jun 13  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  C  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Iron-Binding Protein, Haem-Distal Site Mutation, Cyanide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Pesce, L. Tilleman, J. Donne, E. Aste, P. Ascenzi, C. Ciaccio, M. Coletta, L. Moens, C. Viappiani, S. Dewilde, M. Bolognesi, M. Nardini
Structure And Haem-Distal Site Plasticity In Methanosarcina Acetivorans Protoglobin.
Plos One V. 8 66144 2013
PubMed-ID: 23776624  |  Reference-DOI: 10.1371/JOURNAL.PONE.0066144

(-) Compounds

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

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x):   C
Biological Unit 2 (1x): AB 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1CYN3Ligand/IonCYANIDE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3GOL7Ligand/IonGLYCEROL
4HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5IPA2Ligand/IonISOPROPYL ALCOHOL
Biological Unit 1 (5, 12)
No.NameCountTypeFull Name
1CYN2Ligand/IonCYANIDE ION
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3GOL4Ligand/IonGLYCEROL
4HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5IPA2Ligand/IonISOPROPYL ALCOHOL
Biological Unit 2 (4, 10)
No.NameCountTypeFull Name
1CYN2Ligand/IonCYANIDE ION
2EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3GOL5Ligand/IonGLYCEROL
4HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5IPA1Ligand/IonISOPROPYL ALCOHOL

(-) 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 , LEU 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:146 , ILE A:149 , VAL A:182 , TRP A:185 , CYN A:201 , HOH A:2065 , HOH A:2086 , HOH A:2087BINDING SITE FOR RESIDUE HEM A 200
02AC2SOFTWARETRP A:60 , HEM A:200BINDING SITE FOR RESIDUE CYN A 201
03AC3SOFTWARELEU B:70 , TYR B:73 , PHE B:74 , TYR B:85 , VAL B:89 , ARG B:92 , LEU 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 , VAL B:182 , TRP B:185 , CYN B:201 , HOH B:2083 , HOH B:2084 , HOH B:2109BINDING SITE FOR RESIDUE HEM B 200
04AC4SOFTWARETRP B:60 , HEM B:200BINDING SITE FOR RESIDUE CYN B 201
05AC5SOFTWARELEU C:70 , TYR C:73 , PHE C:74 , TYR C:85 , VAL C:89 , ARG C:92 , LEU 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 , CYN C:201 , HOH C:2074 , HOH C:2075 , HOH C:2095 , HOH C:2096BINDING SITE FOR RESIDUE HEM C 200
06AC6SOFTWARETRP C:60 , HEM C:200BINDING SITE FOR RESIDUE CYN C 201
07AC7SOFTWAREARG B:95 , LEU B:98 , ASN B:102 , HOH B:2053 , HOH B:2086 , GLU C:39 , GLN C:43 , SER C:101 , ASN C:102 , ARG C:103 , SER C:104 , HOH C:2028BINDING SITE FOR RESIDUE EPE C1196
08AC8SOFTWAREASN C:126 , ASN C:130 , VAL C:131 , HOH C:2120BINDING SITE FOR RESIDUE GOL C1197
09AC9SOFTWAREASP A:24 , TYR B:73 , ARG B:140 , HOH B:2131 , HOH B:2132BINDING SITE FOR RESIDUE GOL B1196
10BC1SOFTWAREASN A:82 , LYS A:84 , ASN A:130 , VAL A:131 , GLU A:132 , HOH A:2053 , HOH A:2095 , HOH A:2122 , ALA C:36 , GLU C:37BINDING SITE FOR RESIDUE GOL A1196
11BC2SOFTWARELYS B:29 , PHE B:34 , GLU B:39 , SER B:104 , TYR B:105 , GOL B:1198BINDING SITE FOR RESIDUE GOL B1197
12BC3SOFTWAREHIS A:121 , ARG A:122 , PRO A:164 , HOH A:2108 , HOH A:2123 , TYR B:192 , ASP B:194BINDING SITE FOR RESIDUE GOL A1197
13BC4SOFTWARETHR B:35 , GLU B:37 , SER C:76 , ASN C:82 , VAL C:131 , GLU C:132 , HOH C:2101BINDING SITE FOR RESIDUE GOL C1198
14BC5SOFTWAREGLU B:39 , ILE B:42 , THR B:100 , SER B:101 , ASN B:102 , ARG B:103 , SER B:104 , TYR B:105 , GOL B:1197 , HOH B:2046BINDING SITE FOR RESIDUE GOL B1198
15BC6SOFTWAREARG C:95 , ASN C:102 , HOH C:2078BINDING SITE FOR RESIDUE IPA C1199
16BC7SOFTWAREARG A:122 , PRO A:135 , ASN A:136 , HOH A:2049BINDING SITE FOR RESIDUE IPA A1198

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZJJ)

(-) 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: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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zjj A   6 IPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRLSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195


Chain B 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zjj B   6 IPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRLSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195


Chain C 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zjj C   6 IPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRLSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
   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 3ZJJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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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  3zjj
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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 3zjl 3zjm 3zjn 3zjo 3zjp 3zjq 3zjr 3zjs 3zol 3zom

(-) Related Entries Specified in the PDB File

3zjh TRP(60)B9ALA MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zji TYR(61)B10ALA MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjl LEU(142)G4ALA MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjm ILE(149)G11PHE MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjn M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjo M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH AZIDE
3zjp M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH IMIDAZOLE
3zjq M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH NICOTINAMIDE