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(-) Description

Title :  SOLUTION STRUCTURE OF DNAE INTEIN FROM NOSTOC PUNCTIFORME
 
Authors :  J. S. Oeemig, A. S. Aranko, J. B. Djupsj, H. Iwai
Date :  02 Feb 09  (Deposition) - 19 May 09  (Release) - 19 May 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Intein, Dnae Intein, Protein Splicing, Protein Trans Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. S. Oeemig, A. S. Aranko, J. Djupsjobacka, K. Heinamaki, H. Iwai
Solution Structure Of Dnae Intein From Nostoc Punctiforme: Structural Basis For The Design Of A New Split Intein Suitable For Site-Specific Chemical Modification.
Febs Lett. V. 583 1451 2009
PubMed-ID: 19344715  |  Reference-DOI: 10.1016/J.FEBSLET.2009.03.058
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE III ALPHA SUBUNIT, NUCLEIC ACID BINDING OB-FOLD TRNA/HELICASE-TYPE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainER2566
    Expression System Taxid562
    Expression System VectorPJDJRSF05
    Expression System Vector TypeVECTOR
    GeneDNAE, NPUN_F4872
    MutationYES
    Organism ScientificNOSTOC PUNCTIFORME PCC 73102
    Organism Taxid63737
    Other DetailsFUSION PROTEIN OF N-INTEIN PART FROM DNA POLYMERASE III ALPHA SUBUNIT (RESIDUES 1-102) AND C-INTEIN PART FROM NUCLEIC ACID BINDING OB-FOLD, TRNA/HELICASE-TYPE (RESIDUES 103-137)

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2KEQ)

(-) Sites  (0, 0)

(no "Site" information available for 2KEQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2KEQ)

(-) Sequences/Alignments

NMR Structure
   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:139
 aligned with B2J066_NOSP7 | B2J066 from UniProtKB/TrEMBL  Length:876

    Alignment length:162
                                                                                                                                                        876                                   
                                   759       769       779       789       799       809       819       829       839       849       859       869      |  -         -         -         -  
         B2J066_NOSP7   750 GAAKNGVPKKVADELFEQMLKFAEYCLSYETEILTVEYGLLPIGKIVEKRIECTVYSVDNNGNIYTQPVAQWHDRGEQEVFEYCLEDGSLIRATKDHKFMTVDGQMLPIDEIFERELDLMRVDNLPN-----------------------------------   -
               SCOP domains d2k                       eqa_ A: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...-----------------------ee...eee.....eeehhhhhhh....eeeee.....eeeee..eeee...eeeeeeee....eeeee...eee.....eeehhhhhhhh.............eeeeeeeeee.eeeee.....eee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2keq A  -1 GGA-----------------------LSYETEILTVEYGLLPIGKIVEKRIECTVYSVDNNGNIYTQPVAQWHDRGEQEVFEYCLEDGSLIRATKDHKFMTVDGQMLPIDEIFERELDLMRVDNLPNIKIATRKYLGKQNVYDIGVERDHNFALKNGFIASN 137
                              |      -         -      |  5        15        25        35        45        55        65        75        85        95       105       115       125       135  
                              1                       2                                                                                                                                       

Chain A from PDB  Type:PROTEIN  Length:139
 aligned with B2J821_NOSP7 | B2J821 from UniProtKB/TrEMBL  Length:450

    Alignment length:366
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405      
         B2J821_NOSP7    46 YGYVTYQTAYLKANYPLEYMAALLTANSGDTDKVQRYITNCTNMGISIDPPDINRSGVDFTPTLGKILFGFSAVRNVGQNAIACILEARNETGEFKSLADFCDRVDLRAVNRRTLESLIYCGAFDKIESNRQQLINDSELVYDWAQSRAKDRASGQGNLFDLLGDGFSSTQNKRVNNAFETAPKSKPVTDLPPQKKLQMEKELLGFYVSDHPLKSLRQIAPLLTPINLSQLGEQREDTRLCAVVMLNNVKKVVTKKGDQMAILQIEDLTTQSEAVVFPKTYERISSLLQVDTRLIIWGKVDRRDEQTQFIVEDAEPVETVQMVMVELNPQQAGDMEKLHLLKTILQEHSVDKEKAKMPVIGIIQTE 411
               SCOP domains d2keqa_ A: auto                                                              mated matche                         s                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee...eee....--------------------------------------------------------------.eeehhhhhhh.-------------------------...eeee-------------e.....eeeee..eeee..----------------------------------------------.eeeeeeee...------------------------------.eeeee...eee....---------------.eeehhhhhhhh........------------------------.....eeeeeeeeee.------------eeeee.....eee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2keq A  -1 GGALSYETEILTVEY--------------------------------------------------------------GLLPIGKIVEKR-------------------------IECTVYS-------------VDNNGNIYTQPVAQWHDRG----------------------------------------------EQEVFEYCLEDG------------------------------SLIRATKDHKFMTVDG---------------QMLPIDEIFERELDLMRVDN------------------------LPNIKIATRKYLGKQN------------VYDIGVERDHNFALKNGFIASN 137
                                     8    |    -         -         -         -         -         -       |16        |-         -         -    |   31|        -    |   38        48  |      -         -         -         -        52        62|        -         -         - |      72      |  -         -  |     87        97 |       -         -      |103       113 |       -    |  121       131      
                                         13                                                             14         25                        26    32            33                51                                             52         63                             64             79              80                 99                      100            115          116                     

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2KEQ)

(-) Gene Ontology  (11, 15)

NMR Structure(hide GO term definitions)
Chain A   (B2J821_NOSP7 | B2J821)
molecular function
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.

Chain A   (B2J066_NOSP7 | B2J066)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0016539    intein-mediated protein splicing    The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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        B2J066_NOSP7 | B2J0664kl5 4kl6 4lx3 4qfq
        B2J821_NOSP7 | B2J8214kl5 4kl6 4lx3 4qfq

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