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(-) Description

Title :  RNA LIGASE RTCB/MN2+ COMPLEX
 
Authors :  S. Xia, M. Englert, D. Soll, J. Wang
Date :  26 Feb 12  (Deposition) - 05 Sep 12  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Rna Ligase, Rtcb, Mn2+, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Englert, S. Xia, C. Okada, A. Nakamura, V. Tanavde, M. Yao, S. H. Eom, W. H. Konigsberg, D. Soll, J. Wang
Structural And Mechanistic Insights Into Guanylylation Of Rna-Splicing Ligase Rtcb Joining Rna Between 3'-Terminal Phosphate And 5'-Oh.
Proc. Natl. Acad. Sci. Usa V. 109 15235 2012
PubMed-ID: 22949672  |  Reference-DOI: 10.1073/PNAS.1213795109

(-) Compounds

Molecule 1 - TRNA-SPLICING LIGASE RTCB
    Chains: B, A, C
    EC Number: 6.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: PHO HYP2 INTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x):  B 
Biological Unit 2 (1x): A  
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 30)

Asymmetric Unit (3, 30)
No.NameCountTypeFull Name
1MN6Ligand/IonMANGANESE (II) ION
2SO421Ligand/IonSULFATE ION
3SUC3Ligand/IonSUCROSE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO48Ligand/IonSULFATE ION
3SUC1Ligand/IonSUCROSE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO46Ligand/IonSULFATE ION
3SUC1Ligand/IonSUCROSE
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO47Ligand/IonSULFATE ION
3SUC1Ligand/IonSUCROSE

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS B:17 , ARG B:23 , PRO B:25 , TYR B:57 , LYS B:58 , ASP B:340 , HOH B:987 , HOH B:1013 , HOH B:1017 , HOH B:1171 , HOH B:1218 , HOH B:1234 , HOH B:1239BINDING SITE FOR RESIDUE SUC B 601
02AC2SOFTWAREASP B:95 , CYS B:98 , HIS B:203 , SO4 B:607BINDING SITE FOR RESIDUE MN B 602
03AC3SOFTWARECYS B:98 , HIS B:234 , HIS B:329 , HIS B:404 , HOH B:756 , HOH B:967 , HOH B:970BINDING SITE FOR RESIDUE MN B 603
04AC4SOFTWAREPRO B:128 , SER B:129 , GLY B:130 , VAL B:131 , GLY B:132 , SER B:133 , GLN B:134 , GLY B:135 , ARG B:136 , LYS B:138 , HOH B:708 , HOH B:971BINDING SITE FOR RESIDUE SO4 B 604
05AC5SOFTWAREGLN B:194 , GLY B:199 , SER B:200 , ARG B:238 , ALA B:483 , ALA B:484 , HOH B:717 , HOH B:769 , HOH B:1012 , HOH B:1096BINDING SITE FOR RESIDUE SO4 B 605
06AC6SOFTWAREGLY B:69 , TYR B:70 , ILE B:74 , GLY B:93 , TYR B:94 , LYS B:351 , HOH B:1138 , HOH B:1252BINDING SITE FOR RESIDUE SO4 B 606
07AC7SOFTWAREASP B:95 , CYS B:98 , HIS B:203 , MN B:602 , HOH B:756 , HOH B:758 , HOH B:967 , HOH B:1094 , HOH B:1097 , HOH B:1098BINDING SITE FOR RESIDUE SO4 B 607
08AC8SOFTWARESER B:184 , GLN B:185 , HOH B:744 , HOH B:810BINDING SITE FOR RESIDUE SO4 B 608
09AC9SOFTWAREARG B:366 , ARG B:369 , HOH B:867BINDING SITE FOR RESIDUE SO4 B 609
10BC1SOFTWAREARG A:260 , HOH A:1166 , HIS B:140 , TRP B:141 , HOH B:763BINDING SITE FOR RESIDUE SO4 B 610
11BC2SOFTWARELYS B:212 , ARG B:472BINDING SITE FOR RESIDUE SO4 B 611
12BC3SOFTWARELYS A:17 , ARG A:23 , PRO A:25 , TYR A:57 , LYS A:58 , VAL A:339 , ASP A:340 , HOH A:828 , HOH A:988 , HOH A:1096 , HOH A:1175 , HOH A:1186 , HOH A:1212 , LYS B:125BINDING SITE FOR RESIDUE SUC A 601
13BC4SOFTWAREASP A:95 , CYS A:98 , HIS A:203 , SO4 A:608BINDING SITE FOR RESIDUE MN A 602
14BC5SOFTWARECYS A:98 , HIS A:234 , HIS A:329 , HOH A:764 , HOH A:778 , HOH A:816BINDING SITE FOR RESIDUE MN A 603
15BC6SOFTWARETRP A:162 , GLU A:163 , HOH A:782 , HOH A:813BINDING SITE FOR RESIDUE SO4 A 604
16BC7SOFTWAREGLY A:199 , SER A:200 , HIS A:203 , ARG A:238 , GLY A:239 , HOH A:710 , HOH A:847 , HOH A:1012 , HOH A:1219BINDING SITE FOR RESIDUE SO4 A 605
17BC8SOFTWARETYR A:70 , ILE A:74 , GLY A:93 , TYR A:94 , LYS A:351BINDING SITE FOR RESIDUE SO4 A 606
18BC9SOFTWAREARG A:366 , ARG A:369 , HOH A:862 , HOH A:926BINDING SITE FOR RESIDUE SO4 A 607
19CC1SOFTWAREASP A:95 , HIS A:203 , ASN A:330 , MN A:602 , HOH A:764 , HOH A:816 , HOH A:860 , HOH A:1038 , HOH A:1039 , HOH A:1219BINDING SITE FOR RESIDUE SO4 A 608
20CC2SOFTWARESER A:184 , GLN A:185 , HOH A:793 , HOH A:1135BINDING SITE FOR RESIDUE SO4 A 609
21CC3SOFTWARELYS C:17 , ARG C:23 , PRO C:25 , TYR C:57 , LYS C:58 , ASP C:340 , HOH C:886 , HOH C:911 , HOH C:950 , HOH C:1166 , HOH C:1200 , HOH C:1229BINDING SITE FOR RESIDUE SUC C 601
22CC4SOFTWARECYS C:98 , HIS C:234 , HIS C:329 , HOH C:709 , HOH C:748 , HOH C:912BINDING SITE FOR RESIDUE MN C 602
23CC5SOFTWAREASP C:95 , CYS C:98 , HIS C:203 , SO4 C:608BINDING SITE FOR RESIDUE MN C 603
24CC6SOFTWAREGLY C:69 , TYR C:70 , ILE C:74 , GLY C:93 , TYR C:94 , LYS C:351 , HOH C:746 , HOH C:1057BINDING SITE FOR RESIDUE SO4 C 604
25CC7SOFTWAREGLY C:199 , SER C:200 , HIS C:203 , ARG C:238 , GLY C:239 , HOH C:847 , HOH C:982 , HOH C:996 , HOH C:997 , HOH C:998 , HOH C:1055BINDING SITE FOR RESIDUE SO4 C 605
26CC8SOFTWARETYR C:259 , SER C:275 , GLU C:276 , HOH C:1008BINDING SITE FOR RESIDUE SO4 C 606
27CC9SOFTWAREARG C:366 , ARG C:369 , HOH C:1075BINDING SITE FOR RESIDUE SO4 C 607
28DC1SOFTWAREASP C:95 , CYS C:98 , HIS C:203 , ASN C:330 , MN C:603 , HOH C:746 , HOH C:748 , HOH C:912 , HOH C:971 , HOH C:996 , HOH C:1056BINDING SITE FOR RESIDUE SO4 C 608
29DC2SOFTWARELYS C:212 , ARG C:472 , HOH C:1063BINDING SITE FOR RESIDUE SO4 C 609
30DC3SOFTWARESER C:411 , ARG C:412 , HOH C:811 , HOH C:1038BINDING SITE FOR RESIDUE SO4 C 610

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DWR)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:132 -Ser A:133

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DWR)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.RTCB_PYRHO465-488
 
 		  3A:98-98
B:98-98
C:98-98
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.RTCB_PYRHO465-488
 
 		  1-
B:98-98
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.RTCB_PYRHO465-488
 
 		  1A:98-98
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.RTCB_PYRHO465-488
 
 		  1-
-
C:98-98

(-) Exons   (0, 0)

(no "Exon" information available for 4DWR)

(-) 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:483
 aligned with RTCB_PYRHO | O59245 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:873
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               871   
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871   
           RTCB_PYRHO     2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCLAPGTRVLTEHGYWLKIEEMPEKFKLQRLRVYNIEEGHNDFSKVVFVAEREVGSEEKAIRIVTESGKVIEGSEDHPVLTPEGYVYLRNVKEGDYILVYPFEGVPYEEKKGVILDESAFEGEDPQVVKFLRERNLIPLQWKDPKVGILARILGFALANGYISENDNLTFHGKEEVLREVRKDLEELGIEAIVAEEDKLKVTSREFAFLLEKLGMAHDSIPEWIIEGPLWIKRNFLAGLFGANGSIVEFKGDVPLPITLTHSRELLNDVSRILEGFKVRAKIKMGKNGSYQLVIEDEDSIRNFLGRINYEYDPEKKARGLIAYAYLKFKELMKGNLMTFEEFARDRGYEGGFVAEKVIEVKSVKPEYDKFYDIGVYHSAHNFIANGIVVHNCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG---   -
               SCOP domains d4dwra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee..........eeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeeee......eeeeeeee....eehhhhh.....------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eeeeeeeeeehhhhh.hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhh..........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.eeeeeeeeee..eeeeeeeeee.eee.........hhhhhh...eeee.......eeeee.hhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhh.hhhhhhhhhhhhh..eeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dwr A   2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDIN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKGAAA 484
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481   
                                                                                                                          97                                                                                                                                                                                                                                                                                                                                                                                                     98                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:486
 aligned with RTCB_PYRHO | O59245 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:876
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               871      
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871      
           RTCB_PYRHO     2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCLAPGTRVLTEHGYWLKIEEMPEKFKLQRLRVYNIEEGHNDFSKVVFVAEREVGSEEKAIRIVTESGKVIEGSEDHPVLTPEGYVYLRNVKEGDYILVYPFEGVPYEEKKGVILDESAFEGEDPQVVKFLRERNLIPLQWKDPKVGILARILGFALANGYISENDNLTFHGKEEVLREVRKDLEELGIEAIVAEEDKLKVTSREFAFLLEKLGMAHDSIPEWIIEGPLWIKRNFLAGLFGANGSIVEFKGDVPLPITLTHSRELLNDVSRILEGFKVRAKIKMGKNGSYQLVIEDEDSIRNFLGRINYEYDPEKKARGLIAYAYLKFKELMKGNLMTFEEFARDRGYEGGFVAEKVIEVKSVKPEYDKFYDIGVYHSAHNFIANGIVVHNCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG------   -
               SCOP domains d4dwrb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....eeee..........eeee.hhhhhhhhhh.hhhhhhhhhh........eeeeeeee......eeeeeeee....eehhhhh.....------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eeeee....hhhhhh.hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.eeeeeeeeee..eeeeeeeeee.eee.........hhhhh....eeee.......eeeee.hhhhhhhh..eee.......hhhhhhh..hhhhhhhhhhhh..eee...hhhhhhhhhhhh.hhhhhhhhhhhh...eeeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dwr B   2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDIN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKGAAALEH 487
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481      
                                                                                                                          97                                                                                                                                                                                                                                                                                                                                                                                                     98                                                                                                                                                                                                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:481
 aligned with RTCB_PYRHO | O59245 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:875
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               871     
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871     
           RTCB_PYRHO     2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCLAPGTRVLTEHGYWLKIEEMPEKFKLQRLRVYNIEEGHNDFSKVVFVAEREVGSEEKAIRIVTESGKVIEGSEDHPVLTPEGYVYLRNVKEGDYILVYPFEGVPYEEKKGVILDESAFEGEDPQVVKFLRERNLIPLQWKDPKVGILARILGFALANGYISENDNLTFHGKEEVLREVRKDLEELGIEAIVAEEDKLKVTSREFAFLLEKLGMAHDSIPEWIIEGPLWIKRNFLAGLFGANGSIVEFKGDVPLPITLTHSRELLNDVSRILEGFKVRAKIKMGKNGSYQLVIEDEDSIRNFLGRINYEYDPEKKARGLIAYAYLKFKELMKGNLMTFEEFARDRGYEGGFVAEKVIEVKSVKPEYDKFYDIGVYHSAHNFIANGIVVHNCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG-----   -
               SCOP domains d4dwrc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee..........eeee.hhhhhhhhh..hhhhhhhhhh........eeeeeeee......eeeeeeee....eehhhhh.....------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eeeee....hhhhhh.hhhhhhhhhhhhh....----....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhh......eeeeeee...hhhhhhhhhhhhhhhhhhhhh...........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.eeeeeeeeee..eeeeeeeeee.eee.........hhhhhh...eeee.......eeeee.hhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhh.hhhhhhhhhhhhh..eeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dwr C   2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDIN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGV----RIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKGAAALE 486
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481     
                                                                                                                          97                                                                                                                                                                                                                                                                                                                                                                                                     98                              131  136
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 Classification and Annotation

(-) SCOP Domains  (1, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DWR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DWR)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RTCB_PYRHO | O59245)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0019002    GMP binding    Interacting selectively and non-covalently with GMP, guanosine monophosphate.
    GO:0003972    RNA ligase (ATP) activity    Catalysis of the reaction: ATP + ribonucleotide(n) + ribonucleotide(m) = AMP + diphosphate + ribonucleotide(n+m).
    GO:0008452    RNA ligase activity    Catalysis of the formation of a phosphodiester bond between a hydroxyl group at the end of one RNA chain and the 5'-phosphate group at the end of another.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0000394    RNA splicing, via endonucleolytic cleavage and ligation    Splicing of RNA 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.
    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:0006314    intron homing    Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
    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.

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  4dwr
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  RTCB_PYRHO | O59245
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 Related Entries

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

UniProtKB/Swiss-Prot
        RTCB_PYRHO | O59245: 1uc2 4dwq 4isj 4isz 4it0

(-) Related Entries Specified in the PDB File

4dwq