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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF PROTOGLOBIN FROM METHANOSARCINA ACETIVORANS C2A
 
Authors :  M. Nardini, A. Pesce, L. Thijs, J. A. Saito, S. Dewilde, M. Alam, P. Ascenzi, M. Coletta, C. Ciaccio, L. Moens, M. Bolognesi
Date :  18 Oct 07  (Deposition) - 22 Jan 08  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hemoprotein Structure, Protein Matrix Tunnels, Protoglobin, Methanogenesis, Archaea Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nardini, A. Pesce, L. Thijs, J. A. Saito, S. Dewilde, M. Alam, P. Ascenzi, M. Coletta, C. Ciaccio, L. Moens, M. Bolognesi
Archaeal Protoglobin Structure Indicates New Ligand Diffusion Paths And Modulation Of Haem- Reactivity.
Embo Rep. V. 9 157 2008
PubMed-ID: 18188182  |  Reference-DOI: 10.1038/SJ.EMBOR.7401153

(-) Compounds

Molecule 1 - PROTOGLOBIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY1Ligand/IonOXYGEN MOLECULE
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY2Ligand/IonOXYGEN MOLECULE
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
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 , PHE A:145 , VAL A:182 , TRP A:185 , OXY A:350 , HOH A:2205 , HOH A:2262 , HOH A:2263 , HOH A:2264BINDING 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:2265BINDING SITE FOR RESIDUE PO4 A 202
3AC3SOFTWARETYR A:72 , VAL A:134 , PRO A:135 , ASN A:136 , HOH A:2136 , HOH A:2226 , HOH A:2266 , HOH A:2267BINDING SITE FOR RESIDUE PO4 A 203
4AC4SOFTWAREPRO A:164 , GLU A:165 , TYR A:187 , PRO A:188 , VAL A:190 , LYS A:191 , TYR A:192 , HOH A:2268 , HOH A:2269BINDING SITE FOR RESIDUE GOL A 204
5AC5SOFTWAREPHE A:93 , HEM A:200BINDING SITE FOR RESIDUE OXY A 350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VEB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VEB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VEB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VEB)

(-) Exons   (0, 0)

(no "Exon" information available for 2VEB)

(-) 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 Protoglobin-2vebA01 A:6-195                                                                                                                                                                    Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2veb A   6 IPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
   Legend:   → Mismatch (orange background)
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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 2VEB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VEB)

(-) 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: 2vee 3qzx 3qzz 3r0g 3zh0 3zjh 3zji 3zjj 3zjl 3zjm 3zjn 3zjo 3zjp 3zjq 3zjr 3zjs 3zol 3zom

(-) Related Entries Specified in the PDB File

2vee STRUCTURE OF PROTOGLOBIN FROM METHANOSARCINA ACETIVORANS C2A