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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE TRANSCRIPTIONAL TERMINATOR PROTEIN RHO
 
Authors :  T. J. Allison, T. C. Wood, D. M. Briercheck, F. Rastinejad, J. P. Richardson, G. S. Rule
Date :  05 Mar 98  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription Termination, Termination, Rna Binding Domain, Transcription Regulation, Ob Fold, F1-Atpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Allison, T. C. Wood, D. M. Briercheck, F. Rastinejad, J. P. Richardson, G. S. Rule
Crystal Structure Of The Rna-Binding Domain From Transcription Termination Factor Rho.
Nat. Struct. Biol. V. 5 352 1998
PubMed-ID: 9586995  |  Reference-DOI: 10.1038/NSB0598-352
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO
    Cell Line: BL21
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Gene: RHO
    Expression System Plasmid: PET11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector: T7
    Expression System Vector Type: PLASMID
    Fragment: RNA BINDING DOMAIN, RESIDUES 1 - 130
    Organism Scientific: ESCHERICHIA COLI BL21(DE3)
    Organism Taxid: 469008
    Strain: BL21 (DE3)

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1A62)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A62)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A62)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A62)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1A62)

(-) Exons   (0, 0)

(no "Exon" information available for 1A62)

(-) 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:125
 aligned with RHO_ECO57 | P0AG32 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            RHO_ECO57     1 MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPE 125
               SCOP domains d1a62a1 A:1-47                                 d1a62a2 A:48-125 Rho termination factor, RNA-binding domain                    SCOP domains
               CATH domains -1a62A01 A:2-47                                1a62A02 A:48-117 Nucleic acid-binding proteins                        -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee.....eeee.hhh........eee.hhhhhh.......eeeeee.............eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a62 A   1 mNLTELKNTPVSELITLGENmGLENLARmRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPE 125
                            |       10        20|       30        40        50        60        70        80        90       100       110       120     
                            |                  21-MSE  29-MSE                                                                                            
                            1-MSE                                                                                                                        


Chain A from PDB  Type:PROTEIN  Length:125
 aligned with RHO_ECOL6 | P0AG31 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            RHO_ECOL6     1 MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPE 125
               SCOP domains d1a62a1 A:1-47                                 d1a62a2 A:48-125 Rho termination factor, RNA-binding domain                    SCOP domains
               CATH domains -1a62A01 A:2-47                                1a62A02 A:48-117 Nucleic acid-binding proteins                        -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee.....eeee.hhh........eee.hhhhhh.......eeeeee.............eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a62 A   1 mNLTELKNTPVSELITLGENmGLENLARmRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPE 125
                            |       10        20|       30        40        50        60        70        80        90       100       110       120     
                            1-MSE              21-MSE  29-MSE                                                                                            


Chain A from PDB  Type:PROTEIN  Length:125
 aligned with RHO_ECOLI | P0AG30 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            RHO_ECOLI     1 MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPE 125
               SCOP domains d1a62a1 A:1-47                                 d1a62a2 A:48-125 Rho termination factor, RNA-binding domain                    SCOP domains
               CATH domains -1a62A01 A:2-47                                1a62A02 A:48-117 Nucleic acid-binding proteins                        -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee.....eeee.hhh........eee.hhhhhh.......eeeeee.............eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a62 A   1 mNLTELKNTPVSELITLGENmGLENLARmRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPE 125
                            |       10        20|       30        40        50        60        70        80        90       100       110       120     
                            1-MSE              21-MSE  29-MSE                                                                                            


Chain A from PDB  Type:PROTEIN  Length:125
 aligned with RHO_SHIFL | P0AG33 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            RHO_SHIFL     1 MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPE 125
               SCOP domains d1a62a1 A:1-47                                 d1a62a2 A:48-125 Rho termination factor, RNA-binding domain                    SCOP domains
               CATH domains -1a62A01 A:2-47                                1a62A02 A:48-117 Nucleic acid-binding proteins                        -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee.....eeee.hhh........eee.hhhhhh.......eeeeee.............eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a62 A   1 mNLTELKNTPVSELITLGENmGLENLARmRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPE 125
                            |       10        20|       30        40        50        60        70        80        90       100       110       120     
                            1-MSE              21-MSE  29-MSE
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A62)

(-) Gene Ontology  (14, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RHO_ECOL6 | P0AG31)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008186    RNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain A   (RHO_ECOLI | P0AG30)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008186    RNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A   (RHO_ECO57 | P0AG32)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008186    RNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain A   (RHO_SHIFL | P0AG33)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008186    RNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RHO_ECO57 | P0AG32: 1a63 1a8v 2a8v 5jji 5jjk 5jjl
        RHO_ECOL6 | P0AG31: 1a63 1a8v 2a8v
        RHO_ECOLI | P0AG30: 1a63 1a8v 1pv4 1pvo 1xpo 1xpr 1xpu 2a8v 2ht1 3ice 5jji 5jjk 5jjl
        RHO_SHIFL | P0AG33: 1a63 1a8v 2a8v

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1A62)