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(-) Description

Title :  THE STRUCTURE OF AN ARCHAEAL HOMODIMERIC RNA LIGASE
 
Authors :  M. A. Brooks, L. Meslet-Cladiere, M. Graille, J. Kuhn, K. Blondeau, H. Myllykallio, H. Van Tilbeurgh
Date :  26 May 08  (Deposition) - 03 Jun 08  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna, Ligase, Amppnp, Pab1020, Pyrococcus Abyssi, Nucleotidyl- Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Brooks, L. Meslet-Cladiere, M. Graille, J. Kuhn, K. Blondeau, H. Myllykallio, H. Van Tilbeurgh
The Structure Of An Archaeal Homodimeric Ligase Which Has Rna Circularization Activity.
Protein Sci. V. 17 1336 2008
PubMed-ID: 18511537  |  Reference-DOI: 10.1110/PS.035493.108

(-) Compounds

Molecule 1 - PAB1020
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21 (DE3) RIL
    Expression System Plasmid: PQE-80L
    Expression System Strain: SURE
    Expression System Taxid: 562
    Organism Common: PYROCOCCUS ABYSSI STR. ORSAY
    Organism Scientific: PYROCOCCUS ABYSSI GE5
    Organism Taxid: 272844
    Other Details: EACH MONOMER OF PAB1020 IS BOUND TO ONE MOLECULE OF PHOSPHOAMINO PHOSPHONIC ACID-ADENYLATE ESTER (AMPPNP)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:70 , ILE A:71 , ARG A:73 , GLU A:93 , GLU A:94 , LYS A:95 , VAL A:96 , ASN A:100 , ARG A:115 , GLU A:147 , PHE A:172 , VAL A:200 , ILE A:230 , LYS A:232 , LYS A:241BINDING SITE FOR RESIDUE ANP A 401
2AC2SOFTWAREGLN A:301 , LYS B:284 , PHE B:288 , LYS B:353BINDING SITE FOR RESIDUE MPD A 501
3AC3SOFTWAREVAL A:258 , LEU A:262 , ARG A:362 , TYR A:364BINDING SITE FOR RESIDUE MPD A 502
4AC4SOFTWAREASP A:382 , PHE B:68 , HIS B:70 , ILE B:71 , ARG B:73 , GLU B:93 , GLU B:94 , LYS B:95 , VAL B:96 , ASN B:100 , ARG B:115 , GLU B:147 , PHE B:172 , VAL B:200 , ILE B:230 , LYS B:232 , LYS B:241 , HOH B:2007BINDING SITE FOR RESIDUE ANP B 401
5AC5SOFTWAREGLU B:89 , LYS B:205 , GLU B:345BINDING SITE FOR RESIDUE MPD B 501
6AC6SOFTWAREVAL B:157 , ARG B:362 , TYR B:364BINDING SITE FOR RESIDUE MPD B 502
7AC7SOFTWARETYR B:260 , GLU B:370BINDING SITE FOR RESIDUE MPD B 503
8AC8SOFTWAREARG B:126 , ASP B:129 , LYS B:325 , LYS B:353 , ASP B:354BINDING SITE FOR RESIDUE MRD B 504
9AC9SOFTWAREGLU B:219 , SER B:222 , ILE B:249 , ARG B:290 , GLU B:294BINDING SITE FOR RESIDUE MRD B 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VUG)

(-) 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:373
 aligned with Q9UYG2_PYRAB | Q9UYG2 from UniProtKB/TrEMBL  Length:382

    Alignment length:373
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379   
         Q9UYG2_PYRAB    10 KEILVKLGLTEDRIETLEMKGGIIEDEFDGIRYVRFKDSAGKLRRGTVVIDEEYVIPGFPHIKRIINLRSGIRRIFKRGEFYVEEKVDGYNVRVVMYKGKMLGITRGGFICPFTTERIPDFVPQEFFKDNPNLILVGEMAGPESPYLVEGPPYVKEDIQFFLFDVQEIKTGRSLPVEERLKIAEEYGINHVEVFGKYTKDDVDELYQLIERLSKEGREGIIMKSPDMKKIVKYVTPYANINDIKIGARVFYELPPGYFTSRISRLAFYLAEKRIKGEEFERVAKELGSALLQPFVESIFDVEQEEDIHELFKVRVKRIETAYKMVTHFEKLGLKIEIVDIEEIKDGWRITFKRLYPDATNEIRELIGGKAFVD 382
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh...hhhhhhh....eee.......eee............eeee..eee......eee..hhhhhhhhh...eeeeeee...eeeeeeee..eeeeee.....hhhhhhhhhhh..hhhhhhh..eeeeeeee..................eeeeeeeee.......hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh...eeeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeehhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vug A  10 KEILVKLGLTEDRIETLEMKGGIIEDEFDGIRYVRFKDSAGKLRRGTVVIDEEYVIPGFPHIKRIINLRSGIRRIFKRGEFYVEEKVDGYNVRVVMYKGKMLGITRGGFICPFTTERIPDFVPQEFFKDNPNLILVGEMAGPESPYLVEGPPYVKEDIQFFLFDVQEIKTGRSLPVEERLKIAEEYGINHVEVFGKYTKDDVDELYQLIERLSKEGREGIIMKSPDMKKIVKYVTPYANINDIKIGARVFYELPPGYFTSRISRLAFYLAEKRIKGEEFERVAKELGSALLQPFVESIFDVEQEEDIHELFKVRVKRIETAYKMVTHFEKLGLKIEIVDIEEIKDGWRITFKRLYPDATNEIRELIGGKAFVD 382
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379   


Chain B from PDB  Type:PROTEIN  Length:373
 aligned with Q9UYG2_PYRAB | Q9UYG2 from UniProtKB/TrEMBL  Length:382

    Alignment length:373
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379   
         Q9UYG2_PYRAB    10 KEILVKLGLTEDRIETLEMKGGIIEDEFDGIRYVRFKDSAGKLRRGTVVIDEEYVIPGFPHIKRIINLRSGIRRIFKRGEFYVEEKVDGYNVRVVMYKGKMLGITRGGFICPFTTERIPDFVPQEFFKDNPNLILVGEMAGPESPYLVEGPPYVKEDIQFFLFDVQEIKTGRSLPVEERLKIAEEYGINHVEVFGKYTKDDVDELYQLIERLSKEGREGIIMKSPDMKKIVKYVTPYANINDIKIGARVFYELPPGYFTSRISRLAFYLAEKRIKGEEFERVAKELGSALLQPFVESIFDVEQEEDIHELFKVRVKRIETAYKMVTHFEKLGLKIEIVDIEEIKDGWRITFKRLYPDATNEIRELIGGKAFVD 382
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------DNA_ligase_A_M-2vugB01 B:69-250                                                                                                                                                       ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------DNA_ligase_A_M-2vugB02 B:69-250                                                                                                                                                       ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author hhhhhhhh...hhhhhhh....eee.......eee............eeee..eee......ee...hhhhhhhhh....eeeeee...eeeeeeee..eeeeee.....hhhhhhhhhhh..hhhhhhh..eeeeeeee..................eeeeeeeee.......hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhh...eeeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeehhhhhhhhhhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vug B  10 KEILVKLGLTEDRIETLEMKGGIIEDEFDGIRYVRFKDSAGKLRRGTVVIDEEYVIPGFPHIKRIINLRSGIRRIFKRGEFYVEEKVDGYNVRVVMYKGKMLGITRGGFICPFTTERIPDFVPQEFFKDNPNLILVGEMAGPESPYLVEGPPYVKEDIQFFLFDVQEIKTGRSLPVEERLKIAEEYGINHVEVFGKYTKDDVDELYQLIERLSKEGREGIIMKSPDMKKIVKYVTPYANINDIKIGARVFYELPPGYFTSRISRLAFYLAEKRIKGEEFERVAKELGSALLQPFVESIFDVEQEEDIHELFKVRVKRIETAYKMVTHFEKLGLKIEIVDIEEIKDGWRITFKRLYPDATNEIRELIGGKAFVD 382
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379
   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 2VUG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DNA_ligase (17)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9UYG2_PYRAB | Q9UYG2)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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  2vug
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