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(-) Description

Title :  STRUCTURE DETERMINATION OF THE DIMERIC ENDONUCLEASE IN A PSEUDO-FACE-CENTERD P21 SPACE GROUP
 
Authors :  H. Li, Y. Zhang
Date :  23 Sep 03  (Deposition) - 09 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna Splicing; Endonuclease; X-Ray Crystallography, Translation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, H. Li
Structure Determination Of A Truncated Dimeric Splicing Endonuclease In Pseudo-Face-Centered Space Group P2(1)2(1)2
Acta Crystallogr. , Sect. D V. 60 447 2004
PubMed-ID: 14993668  |  Reference-DOI: 10.1107/S0907444903029482

(-) Compounds

Molecule 1 - TRNA-INTRON ENDONUCLEASE
    Chains: A, B
    EC Number: 3.1.27.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ENDA
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304
    Synonym: SPLICING ENDONUCLEASE;
INTRON ENDONUCLEASE;
ENDA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1R11)

(-) Sites  (0, 0)

(no "Site" information available for 1R11)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R11)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R11)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R11)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R11)

(-) Exons   (0, 0)

(no "Exon" information available for 1R11)

(-) 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:303
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:303
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302   
           ENDA_ARCFU     3 GGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains d1r11a3 A:3-60                                            d1r11a1 A:61-139 Dimeric tRNA splicing endonuclease, domains 2 and 4           d1r11a4 A:140-214 Dimeric tRNA splicing endonuclease, domains 1 and 3      d1r11a2 A:215-305 Dimeric tRNA splicing endonuclease, domains 2 and 4                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhhh....ee...eeeehhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhh....eee..eee...eeeeee...eehhhhhhh........eeeee.....eeeeeee..............eeeee....eee..hhhhhh....eee..eeeehhhhhhhhhhh..eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee....hhhhhhhh.eeeee.....eehhhhhhhhhhhhhh..eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r11 A   3 GGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302   


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:303
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302   
           ENDA_ARCFU     3 GGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains d1r11b3 B:3-60                                            d1r11b1 B:61-139 Dimeric tRNA splicing endonuclease, domains 2 and 4           d1r11b4 B:140-214 Dimeric tRNA splicing endonuclease, domains 1 and 3      d1r11b2 B:215-305 Dimeric tRNA splicing endonuclease, domains 2 and 4                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------tRNA_int_endo_N-1r11B03 B:149-209                            ------tRNA_int_endo-1r11B01 B:216-299                                                     ------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------tRNA_int_endo_N-1r11B04 B:149-209                            ------tRNA_int_endo-1r11B02 B:216-299                                                     ------ Pfam domains (2)
         Sec.struct. author ....eeee.hhhhhh....eee..eeeehhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhh....eee..eee...eeeeee...eehhhhhhhhhh.....eeeee.....eeeeeee..............eeeee....eee..hhhhhh....eee..eeeehhhhhhhhhhh..eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee....hhhhh....eeeee.....eehhhhhhhhhhhhhh..eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r11 B   3 GGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R11)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: tRNA-IECD (4)
(-)
Clan: tRNA-IECD_N (2)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        ENDA_ARCFU | O29362: 1r0v 1rlv 2gjw 3p1y

(-) Related Entries Specified in the PDB File

1r0v THE SAME PROTEIN IN DIFFERENT SPACE GROUP