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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHIMERIC ARCHAEOGLOBUS FULGIDUS RNA SPLICING ENDONUCLEASE WITH THE BROADEST SUBSTRATE SPECIFICITY
 
Authors :  A. Hirata
Date :  01 Oct 10  (Deposition) - 10 Aug 11  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Protein Homodimer, Rna Splicing Endonuclease, Broad Substrate Specificity, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hirata, T. Kitajima, H. Hori
Cleavage Of Intron From The Standard Or Non-Standard Position Of The Precursor Trna By The Splicing Endonuclease Of Aeropyrum Pernix, A Hyper-Thermophilic Crenarchaeon, Involves A Novel Rna Recognition Site In The Crenarchaea Specific Loop
Nucleic Acids Res. V. 39 9376 2011
PubMed-ID: 21846775  |  Reference-DOI: 10.1093/NAR/GKR615

(-) Compounds

Molecule 1 - TRNA-SPLICING ENDONUCLEASE
    Chains: A, B, C, D
    EC Number: 3.1.27.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS, AEROPYRUM PERNIX, ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234, 56636, 2234
    Other Details: CHIMERA PROTEIN OF TRNA-SPLICING ENDONUCLEASE FROM ARCHAEOGLOBUS FULGIDUS (UNP RESIDUES 2-173), A INSERTION OF UNP RESIDUES 39-53 OF TRNA-SPLICING ENDONUCLEASE FROM AEROPYRUM PERNIX, TRNA-SPLICING ENDONUCLEASE FROM ARCHAEOGLOBUS FULGIDUS (UNP RESIDUES 179-188)
    Synonym: TRNA-INTRON ENDONUCLEASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3P1Y)

(-) Sites  (0, 0)

(no "Site" information available for 3P1Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P1Y)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Phe A:185 -Glu A:186
2Gly A:187 -Pro A:188
3Gly B:187 -Pro B:188
4Gly C:187 -Pro C:188
5Gly D:187 -Pro D:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3P1Y)

(-) 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:314
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:314
                                                                                                                                                                                                           175                                                                                                                                        
                                                                                                                                                                                                     173  174|    176                                                                                                                                 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 |    || -    |  181       191       201       211       221       231       241       251       261       271       281       291       301    
           ENDA_ARCFU     2 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGS----EK------GDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhhh..eee..eeeehhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eee..eee...eeeeee...eehhhhhhhhhh.....eeeee.....eeeeeee..............eeeeee..eeee..hhhhhh....ee..............eeehhhhhhhhhh...eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee....hhhhh....eeeee.....eehhhhhhhhhhhhhh..eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1y A   2 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSPLDVEKPRGADFEGPVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311    


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:314
                                                                                                                                                                                                           175                                                                                                                                        
                                                                                                                                                                                                     173  174|    176                                                                                                                                 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 |    || -    |  181       191       201       211       221       231       241       251       261       271       281       291       301    
           ENDA_ARCFU     2 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGS----EK------GDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhh....eee..eeeehhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eee..eee...eeeeee...eehhhhhhhhhhhh...eeeee.....eeeeeee..............eeeeee..eeee..hhhhhh....ee..............eeehhhhhhhhhhh..eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee....hhhhhhhh.eeeee.....eehhhhhhhhhhhhhh..eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1y B   2 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSPLDVEKPRGADFEGPVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311    


Chain C from PDB  Type:PROTEIN  Length:314
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:314
                                                                                                                                                                                                           175                                                                                                                                        
                                                                                                                                                                                                     173  174|    176                                                                                                                                 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 |    || -    |  181       191       201       211       221       231       241       251       261       271       281       291       301    
           ENDA_ARCFU     2 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGS----EK------GDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhh...eee..eeeehhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eee..eee...eeeeee...eehhhhhhhhhh.....eeeee.....eeeeeee..............eeeeee..eeee..hhhhhh....ee..............eeehhhhhhhhhhh..eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee....hhhhh....eeeee.....eehhhhhhhhhhhhhh..eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1y C   2 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSPLDVEKPRGADFEGPVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311    


Chain D from PDB  Type:PROTEIN  Length:314
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:314
                                                                                                                                                                                                           175                                                                                                                                        
                                                                                                                                                                                                     173  174|    176                                                                                                                                 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 |    || -    |  181       191       201       211       221       231       241       251       261       271       281       291       301    
           ENDA_ARCFU     2 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGS----EK------GDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhhh..eee..eeeehhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eee..eee...eeeeee...eehhhhhhhhhh.....eeeee.....eeeeeee..............eeeeee..eeee..hhhhhh....ee..............eeehhhhhhhhhhh..eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee.......hhhhh.eeeee.....eehhhhhhhhhhhhhh..eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1y D   2 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSPLDVEKPRGADFEGPVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
   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 3P1Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P1Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P1Y)

(-) Gene Ontology  (9, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ENDA_ARCFU | O29362)
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.

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  Cis Peptide Bonds
    Gly A:187 - Pro A:188   [ RasMol ]  
    Gly B:187 - Pro B:188   [ RasMol ]  
    Gly C:187 - Pro C:188   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ENDA_AERPE | Q9YBF1: 3ajv 3p1z
        ENDA_ARCFU | O29362: 1r0v 1r11 1rlv 2gjw

(-) Related Entries Specified in the PDB File

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