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(-) Description

Title :  RNA RECOGNITION AND CLEAVAGE BY AN SPLICING ENDONUCLEASE
 
Authors :  S. Xue, K. Calvin, H. Li
Date :  31 Mar 06  (Deposition) - 12 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D,E,F,H,I,J,L
Biol. Unit 1:  A,B,E,F,H  (1x)
Biol. Unit 2:  C,D,I,J,L  (1x)
Keywords :  Bulge-Helix-Bulge Rna-Protein Complex, Splicing Endonuclease Af, Hydrolase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Xue, K. Calvin, H. Li
Rna Recognition And Cleavage By An Splicing Endonuclease
Science V. 312 902 2006
PubMed-ID: 16690865  |  Reference-DOI: 10.1126/SCIENCE.1126629
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU) P*AP*GP*CP*UP*GP*CP*A)-3'
    Chains: E, I
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3'
    Chains: F, J
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-R(*AP*GP*GP*UP*CP*GP*C)-3'
    Chains: H, L
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - TRNA-SPLICING ENDONUCLEASE
    Chains: A, B, C, D
    EC Number: 3.1.27.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET13B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ENDA
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: TRNA-INTRON ENDONUCLEASE

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFHIJL
Biological Unit 1 (1x): AB  EFH   
Biological Unit 2 (1x):   CD   IJL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1A232Mod. NucleotideADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2DU2Mod. Residue
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1A231Mod. NucleotideADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2DU-1Mod. Residue
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1A231Mod. NucleotideADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2DU-1Mod. Residue

(-) Sites  (0, 0)

(no "Site" information available for 2GJW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GJW)

(-) 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:308
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:308
                               1                                                                                                                                                                                                                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297        
           ENDA_ARCFU     - ---MIGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains ----d2gjwa3 A:5-63                                             d2gjwa1 A:64-142 Dimeric tRNA splicing endonuclease, domains 2 and 4           d2gjwa4 A:143-217 Dimeric tRNA splicing endonuclease, domains 1 and 3      d2gjwa2 A:218-308 Dimeric tRNA splicing endonuclease, domains 2 and 4                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.hhhhhhh...eee..eeeehhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eee..eee...eeeeee...eehhhhhhhhhhhh...eeeee.....eeeeeee..............eeeeee..eeee..hhhhhh....eee..eeeeehhhhhhhhhh..eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee.............eeeee.....eehhhhhhhhhhhhhh..eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gjw A   1 HHHHIGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        


Chain B from PDB  Type:PROTEIN  Length:304
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:304
                                    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 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains d2gjwb3 B:4-62                                             d2gjwb1 B:63-141 Dimeric tRNA splicing endonuclease, domains 2 and 4           d2gjwb4 B:142-216 Dimeric tRNA splicing endonuclease, domains 1 and 3      d2gjwb2 B:217-307 Dimeric tRNA splicing endonuclease, domains 2 and 4                       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..........eeeehhhhhhhhhh..eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee.............eeeee.....eehhhhhhhhhhhhhh..eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gjw B   4 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303    


Chain C from PDB  Type:PROTEIN  Length:307
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:307
                              1                                                                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       
           ENDA_ARCFU     - --MIGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains ---d2gjwc3 C:4-62                                             d2gjwc1 C:63-141 Dimeric tRNA splicing endonuclease, domains 2 and 4           d2gjwc4 C:142-216 Dimeric tRNA splicing endonuclease, domains 1 and 3      d2gjwc2 C:217-307 Dimeric tRNA splicing endonuclease, domains 2 and 4                       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..............eeeee...eeee..hhhhhh....ee....eeeehhhhhhhhhh..eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee.............eeeee.....eehhhhhhhhhhhhhh..eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gjw C   1 HHHIGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       


Chain D from PDB  Type:PROTEIN  Length:304
 aligned with ENDA_ARCFU | O29362 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:304
                                    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 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 305
               SCOP domains d2gjwd3 D:5-63                                             d2gjwd1 D:64-142 Dimeric tRNA splicing endonuclease, domains 2 and 4           d2gjwd4 D:143-217 Dimeric tRNA splicing endonuclease, domains 1 and 3      d2gjwd2 D:218-308 Dimeric tRNA splicing endonuclease, domains 2 and 4                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhh...eee..eeeehhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eee..eee...eeeeee...eehhhhhhhhhhhh...eeeee.....eeeeee...............eeeeee..eeee..hhhhhh....eee..eeeeehhhhhhhhhh..eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee.............eeeee.....eehhhhhhhhhhhhh...eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gjw D   5 IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV 308
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    


Chain E from PDB  Type:DNA/RNA  Length:18
                                                  
                 2gjw E   3 GCGACCGACCAxAGCUGC  20
                                    12 |      
                                      14-DU   


Chain F from PDB  Type:RNA  Length:12
                                            
                 2gjw F   3 UGCAGCGGUCAa  14
                                    12 |
                                      14-A23


Chain H from PDB  Type:RNA  Length:7
                                       
                 2gjw H  15 AGGUCGC  21


Chain I from PDB  Type:DNA/RNA  Length:19
                                                   
                 2gjw I   3 GCGACCGACCAxAGCUGCA  21
                                    12 |       
                                      14-DU    


Chain J from PDB  Type:RNA  Length:12
                                            
                 2gjw J   3 UGCAGCGGUCAa  14
                                    12 |
                                      14-A23


Chain L from PDB  Type:RNA  Length:7
                                       
                 2gjw L  15 AGGUCGC  21
   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, 16)

Asymmetric 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 2GJW)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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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  2gjw
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENDA_ARCFU | O29362: 1r0v 1r11 1rlv 3p1y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GJW)