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(-) Description

Title :  CRYSTAL STRUCTURE OF RTCA, THE RNA 3'-TERMINAL PHOSPHATE CYCLASE FROM PYROCOCCUS HORIKOSHII, IN COMPLEX WITH RACAAA3'PHOSPHATE AND ADENINE.
 
Authors :  K. K. Desai, C. A. Bingman, G. N. Phillips Jr, R. T. Raines
Date :  27 Dec 13  (Deposition) - 10 Sep 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  3' Rna Cyclase, Rna, Ligase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. K. Desai, C. A. Bingman, C. L. Cheng, G. N. Phillips, R. T. Raines
Structure Of Rna 3'-Phosphate Cyclase Bound To Substrate Rna.
Rna V. 20 1560 2014
PubMed-ID: 25161314  |  Reference-DOI: 10.1261/RNA.045823.114

(-) Compounds

Molecule 1 - RNA 3'-TERMINAL PHOSPHATE CYCLASE
    Chains: A, B
    EC Number: 6.5.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: PH1529, PHCV028, RTCA
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
    Synonym: RNA CYCLASE, RNA-3'-PHOSPHATE CYCLASE
 
Molecule 2 - RNA
    Chains: D, E
    Engineered: YES
    Other Details: SYNTHETIC RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): A  E
Biological Unit 2 (1x):  BD 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:14 , ARG A:17 , LEU A:97 , GLN A:100 , PRO A:127 , ASP A:250 , PHE A:283 , ASP A:286 , GLN A:287 , HIS A:307 , A E:6BINDING SITE FOR RESIDUE ADN A 401
2AC2SOFTWAREGLN B:14 , LEU B:97 , GLN B:100 , SER B:126 , PRO B:127 , ASP B:250 , PHE B:283 , ASP B:286 , GLN B:287 , HIS B:307 , HOH B:740BINDING SITE FOR RESIDUE ADN B 401
3AC3SOFTWAREVAL B:63 , LYS B:64 , GLY B:65 , ALA B:66 , LYS B:180 , GLU B:181 , TRP B:300 , HOH B:707 , HOH B:711BINDING SITE FOR RESIDUE EPE B 402

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:244 -A:279
2B:244 -B:279

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:157 -Pro A:158
2Tyr B:157 -Pro B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O8J)

(-) Exons   (0, 0)

(no "Exon" information available for 4O8J)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee........eeee........eeee.....hhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhhh...eeeeeee........eeeeeee........eee.....eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhhh..eeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o8j A   1 MITIDGSYGEGGGQILRTSVALSTITGEPVRIVNIRANRPNPGLRPQHLHAILALKHLANAEVKGAHVGSRELVFIPKKLEAKEISIDIGTAGSITLVLQALLPAMVFAREKVKFRITGGTDVSWSPPVDYLSNVTLFALEKIGIHGEIRVIRRGHYPKGGGIVEGYVEPWNEKRELVAKEYSRIIKIEGISHATNLPSHVAERQARAAKDELLQLKVPIEIRTEISRSIGPGSGIVVWAETDCLRLGGDALGKKGKPAEIVGKEAAQELLDQLKPGHCVDKFLGDQLIPFLAFSGGVIWVSEITNHLKTNIWVVESFLGRIFDVDGNVGEPGKIRVIRRV 341
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Chain B from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee........eeee........eeee.....hhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhhh...eeeeeee........eeeeeee........eee.....eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhhh..eeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o8j B   1 MITIDGSYGEGGGQILRTSVALSTITGEPVRIVNIRANRPNPGLRPQHLHAILALKHLANAEVKGAHVGSRELVFIPKKLEAKEISIDIGTAGSITLVLQALLPAMVFAREKVKFRITGGTDVSWSPPVDYLSNVTLFALEKIGIHGEIRVIRRGHYPKGGGIVEGYVEPWNEKRELVAKEYSRIIKIEGISHATNLPSHVAERQARAAKDELLQLKVPIEIRTEISRSIGPGSGIVVWAETDCLRLGGDALGKKGKPAEIVGKEAAQELLDQLKPGHCVDKFLGDQLIPFLAFSGGVIWVSEITNHLKTNIWVVESFLGRIFDVDGNVGEPGKIRVIRRV 341
                                    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       310       320       330       340 


Chain D from PDB  Type:DNA/RNA  Length:6
                                      
                 4o8j D   1 ACAAAA   6


Chain E from PDB  Type:DNA/RNA  Length:6
                                      
                 4o8j E   1 ACAAAA   6
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  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 4O8J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O8J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O8J)

(-) Gene Ontology  (7, 7)

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 Related Entries

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        RTCA_PYRHO | O59198: 4o89

(-) Related Entries Specified in the PDB File

4089