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(-) Description

Title :  STRUCTURE OF A BACTERIAL RIBONUCLEASE P HOLOENZYME IN COMPLEX WITH TRNA
 
Authors :  N. J. Reiter, A. Osterman, A. Torres-Larios, K. K. Swinger, T. Pan, A. Mo
Date :  17 Dec 10  (Deposition) - 09 Mar 11  (Release) - 09 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rnase P, Ribozyme, Ribonuclease P, Trna, Pre-Trna, Tetraloop- Receptor, Ribose Zipper, A-Minor Interaction, Base Stacking, Intermolecular Base Pairs, Intermolecular Rna-Rna Contacts, Rnp, Ribonucleoprotein Complex, Enzyme-Product Complex, Metalloenzyme, Rna-Metal Interactions, Shape Complementarity, Hydrolase-Rna Complex, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. J. Reiter, A. Osterman, A. Torres-Larios, K. K. Swinger, T. Pan, A. Mondragon
Structure Of A Bacterial Ribonuclease P Holoenzyme In Complex With Trna.
Nature V. 468 784 2010
PubMed-ID: 21076397  |  Reference-DOI: 10.1038/NATURE09516

(-) Compounds

Molecule 1 - RNASE P RNA
    Chains: B
    Engineered: YES
    Other Details: THE RNA WAS PREPARED BY IN VITRO TRANSCRIPTION
    Synthetic: YES
 
Molecule 2 - RIBONUCLEASE P PROTEIN COMPONENT
    Chains: A
    EC Number: 3.1.26.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T-2
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Gene: RNPA, RNPA OR TM1463, RNPB, TM_1463
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: RNASE P PROTEIN, RNASEP PROTEIN, PROTEIN C5
 
Molecule 3 - TRNA (PHE)
    Chains: C
    Engineered: YES
    Other Details: THE RNA WAS PREPARED BY IN VITRO TRANSCRIPTION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA C:83 , C C:84BINDING SITE FOR RESIDUE MG C 901
2AC2SOFTWAREA B:150 , G B:151BINDING SITE FOR RESIDUE MG B 902
3AC3SOFTWAREA B:50 , G B:51 , U B:52 , G C:1BINDING SITE FOR RESIDUE MG B 903
4AC4SOFTWAREG B:1 , G B:347BINDING SITE FOR RESIDUE MG B 904
5AC5SOFTWAREARG A:52 , G C:1BINDING SITE FOR RESIDUE PO4 A 118
6AC6SOFTWAREARG A:89 , LYS A:90BINDING SITE FOR RESIDUE PO4 A 119

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q1Q)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:116 -Gly A:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q1Q)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68  1A:54-68

(-) Exons   (0, 0)

(no "Exon" information available for 3Q1Q)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:112
 aligned with RNPA_THEMA | Q9X1H4 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:112
                                    15        25        35        45        55        65        75        85        95       105       115  
           RNPA_THEMA     6 TRRERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGLDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Ribonuclease_P-3q1qA01 A:6-116                                                                                 - Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhheeee...eeeeeee......eeee..hhhh..hhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------RIBONUCLEASE_P ------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3q1q A   6 TRRERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGLDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
                                    15        25        35        45        55        65        75        85        95       105       115  


Chain B from PDB  Type:DNA/RNA  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
                 3q1q B   1 GGAGAGGAGCAGGCGGUCGCGGGGGCGCACACCUGCGCUUCCCGAGGAAAGUCCGGACUCUGGAGCGGGGUGCCGGGUAACGCCCGGGAGGGGUGACCCUCGGACAGGGCCAUAGAGAAGAAGACCGCCCGGGGGGAAACUUCCGGGCAAGGGUGGAACGGUGGGGUAAGAGCCCACCAGCGUCGGGGCAACCCGGCGGCUUGGCAACCCCCACCUGGAGCAAGGCCAAGCAGGGGGUUGGGUCGCUCCCCCUAUUCCCCCGGGUUGGCCGCUUGAGGUGUGCGGUAACGCACACCCCAGAUUGAUGACCGCCCACGACAGAAUCCGGCUUAUGCUCCUCUCCCGUG 347
                                    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 C from PDB  Type:DNA/RNA  Length:86
                                                                                                                      
                 3q1q C   1 GGCCAGGUAGCUCAGUUGGUAGAGCACUGGAUAUGGGCACCCCCUAAGUCCAGGUGUCGGCGGUUCGAUUCCGCCCCUGGCCACCA  86
                                    10        20        30        40        50        60        70        80
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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 3Q1Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q1Q)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: S5 (103)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNPA_THEMA | Q9X1H4)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004526    ribonuclease P activity    Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
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:0001682    tRNA 5'-leader removal    Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        RNPA_THEMA | Q9X1H4: 1nz0 3q1r

(-) Related Entries Specified in the PDB File

1ehz 1nbs 1nz0 1u9s 2a2e 2a64 3q1r