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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FUNCTIONAL NANOARCHAEUM EQUITANS TRNA SPLICING ENDONUCLEASE
 
Authors :  M. Mitchell, H. Li
Date :  23 Jul 09  (Deposition) - 01 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Protein Heterodimer, Endonuclease, Hydrolase, Nuclease, Trna Processing, Hydrolase-Rna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mitchell, S. Xue, R. Erdman, L. Randau, D. Soll, H. Li
Crystal Structure And Assembly Of The Functional Nanoarchaeum Equitans Trna Splicing Endonuclease.
Nucleic Acids Res. V. 37 5793 2009
PubMed-ID: 19578064  |  Reference-DOI: 10.1093/NAR/GKP537

(-) Compounds

Molecule 1 - TRNA-SPLICING ENDONUCLEASE
    Chains: A
    EC Number: 3.1.27.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-DUET
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ENDA, NEQ205
    Mutation: YES
    Organism Scientific: NANOARCHAEUM EQUITANS
    Organism Taxid: 160232
    Synonym: TRNA-INTRON ENDONUCLEASE
 
Molecule 2 - NEQ261
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-DUET
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NEQ261
    Organism Scientific: NANOARCHAEUM EQUITANS
    Organism Taxid: 160232

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3IEY)

(-) Sites  (0, 0)

(no "Site" information available for 3IEY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Val A:90 -Ile A:91
2Arg A:97 -Ser A:98
3Ser B:151 -Asn B:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IEY)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:147
 aligned with ENDA_NANEQ | Q74MP4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           ENDA_NANEQ     2 IGYLFGNRVLVDDKELPLIEAYYLLDKGELEVYEDDKKLSKEEFLKKCLTYDERFLIRYKAYKELRDKGYTLGTALKFGADFRVYDIGVIPKKGKRSEREHSKWVLYPVSKDETFDFYEFASKNRVAHSTRKKLLLGIVSDKIEFIEVSWKKP 154
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee..--.eehhhhhhhhhhh........----hhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeehhhheeeeee...................eeeeee...eeehhhhhhhhhhhhhh...eeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iey A   2 IGYLFGNRVLVD--ELPLIEAYYLLDKGELEVYEDD----KEEFLKKCLTYDERFLIRYKAYKELRDKGYTLGTALKFGADFRVYDIGVIPKKGKRSEREHSKWVLYPVSKDETFDFYEFASKNRVAHSTRKKMLMGIVSDKIEFIEVSWKKP 154
                                    11 |  |   21        31     |   -|       51        61        71        81        91       101       111       121       131       141       151   
                                      13 16                   37   42                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:152
 aligned with Q74MS9_NANEQ | Q74MS9 from UniProtKB/TrEMBL  Length:153

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
         Q74MS9_NANEQ     1 MNLRIPWKEVYYLGYNMGNYIKISEPELLFVLRNKPQIKDRLKLDEKTIIKEGVKKYKNFWEIYYTVKDLILRGYRVRFDGFFIELYEKGIIPGTIEQDYLVYPVSGEIRMTWGELLDIYNKAIARKSKFMLAIVDSEGDVTYYEFRKLRSN 152
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhh...ee....ee.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee....eeee............eeeeeee...eeehhhhhhhhhhhhhh..eeeeeee.....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iey B   1 MNLRIPWKEVYYLGYNMGNYIKISEPELLFVLRNKPQIKDRLKLDEKTIIKEGVKKYKNFWEIYYTVKDLILRGYRVRFDGFFIELYEKGIIPGTIEQDYLVYPVSGEIRMTWGELLDIYNKAIARKSKFMLAIVDSEGDVTYYEFRKLRSN 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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 3IEY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (ENDA_NANEQ | Q74MP4)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000213    tRNA-intron endonuclease activity    Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0006388    tRNA splicing, via endonucleolytic cleavage and ligation    Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.

Chain B   (Q74MS9_NANEQ | Q74MS9)
molecular function
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000213    tRNA-intron endonuclease activity    Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006388    tRNA splicing, via endonucleolytic cleavage and ligation    Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.

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 Related Entries

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