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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF RLUB IN COMPLEX WITH A 21-NUCLEOTIDE RNA SUBSTRATE
 
Authors :  N. Czudnochowski, J. S. Finer-Moore, R. M. Stroud
Date :  28 Jun 13  (Deposition) - 20 Nov 13  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,D,E,F
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  D,F  (1x)
Keywords :  Beta Sheet Alpha-Beta Protein, Rrna Modification Peudouridine Synthase, E. Coli Ribosomal Rna, Isomerase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Czudnochowski, G. W. Ashley, D. V. Santi, A. Alian, J. Finer-Moore, R. M. Stroud
The Mechanism Of Pseudouridine Synthases From A Covalent Complex With Rna, And Alternate Specificity For U2605 Versu U2604 Between Close Homologs.
Nucleic Acids Res. V. 42 2037 2014
PubMed-ID: 24214967  |  Reference-DOI: 10.1093/NAR/GKT1050

(-) Compounds

Molecule 1 - RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE B
    Chains: A, D
    EC Number: 5.4.99.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET47 MODIFIED
    Expression System Strain: BL21(DE)3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-251
    Gene: RLUB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
 
Molecule 2 - STEM-LOOP OF 23S RRNA
    Chains: E, F
    Engineered: YES
    Other Details: 21-MER WITH THE SAME SEQUENCE AS STEM-LOOP NT 2587- 2607 FROM E. COLI 23S RRNA SYNTHESIZED WITH U2605 SUBSTITUTED BY 5- FLUOR-U2605
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ADEF
Biological Unit 1 (1x): A E 
Biological Unit 2 (1x):  D F

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FHU2Mod. Nucleotide(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5'-MONOPHOSPHATE
2OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FHU1Mod. Nucleotide(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5'-MONOPHOSPHATE
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FHU1Mod. Nucleotide(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5'-MONOPHOSPHATE
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) 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:251
                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhh...hhhhhhhhhhh..eee..ee.....ee.......eee..ee............eeeeee.............................ee........eeeeeee.hhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhheee..eee...eeeeeeee..eeeeeeee.....hhhhhhhhhh..eeeeeeeeee..ee.........eee.hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lgt A    1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTcGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRELVELPPETS  251
                                    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 
                                                                                                                                           114-OCS                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhh...hhhhhhhhhhh..eee..ee.....ee.......eee..eee........eeeeee.............................ee........eeeeeee.hhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhheee..eee...eeeeee....eeeeeeee.....hhhhhhhhhh..eeeeeeeeee..ee.........eee.hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lgt D    1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTcGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRELVELPPET  250
                                    10        20        30        40        50        60 ||     73        83        93       103       113|      123       133       143       153       163       173       183       193       203       213       223       233       243       
                                                                                        62|                                             114-OCS                                                                                                                                    
                                                                                         66                                                                                                                                                                                        


Chain E from PDB  Type:RNA  Length:21
                                                      
                4lgt E 2587 AGAACGUCGUGAGACAGUuCG 2607
                                  2596      2606 
                                           2605-FHU


Chain F from PDB  Type:RNA  Length:20
                                                     
                4lgt F 2588 GAACGUCGUGAGACAGUuCG 2607
                                  2597      2607
                                          2605-FHU
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 Classification and Annotation

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(-) Gene Ontology  (10, 10)

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 Related Entries

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        RLUB_ECOLI | P37765: 4lab

(-) Related Entries Specified in the PDB File

4lab STRUCTURE OF APO RLUB CATALYTIC DOMAIN