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(-) Description

Title :  STRUCTURE OF THE RNA-PROCESSING INHIBITOR RRAA FROM THERMUS THERMOPHILIS
 
Authors :  P. H. Rehse, M. Miyano, T. H. Tahirov, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Feb 03  (Deposition) - 17 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Vitamine K2, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. H. Rehse, C. Kuroishi, T. H. Tahirov
Structure Of The Rna-Processing Inhibitor Rraa From Thermus Thermophilis.
Acta Crystallogr. , Sect. D V. 60 1997 2004
PubMed-ID: 15502308  |  Reference-DOI: 10.1107/S0907444904021146
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEMETHYLMENAQUINONE METHYLTRANSFERASE
    ChainsA, B, C, D, E, F
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid274
    StrainHD8

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:155 , ASP D:97 , GLU D:100 , HOH D:191BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWAREGLY A:74 , ASN A:76 , LEU A:77BINDING SITE FOR RESIDUE CL A 1002
3AC3SOFTWAREHOH A:1011 , ARG B:28 , ALA B:29 , ARG B:30 , HOH B:1049BINDING SITE FOR RESIDUE CL B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J3L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J3L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J3L)

(-) Exons   (0, 0)

(no "Exon" information available for 1J3L)

(-) 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:164
 aligned with RRAAH_THET8 | Q5SIP7 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
          RRAAH_THET8     1 MEARTTDLSDLYPEGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARLAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVRSGG 164
               SCOP domains d1j3la_ A: Demethylmenaquinone methyltransferase                                                                                                                     SCOP domains
               CATH domains 1j3lA00 A:1-164  [code=3.50.30.40, no name defined]                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh...eee....ee......eeeeeeeee....hhhhhhhhh.....eeeeee..........hhhhhhhhhhh...eeeee.ee.hhhhhh....eeee.ee...........ee...eee..eee....eeeee..eeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3l A   1 MEARTTDLSDLYPEGEALPmVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVRSGG 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
                                              20-MSE                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with RRAAH_THET8 | Q5SIP7 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
          RRAAH_THET8     1 MEARTTDLSDLYPEGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARLAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVRSGG 164
               SCOP domains d1j3lb_ B: Demethylmenaquinone methyltransferase                                                                                                                     SCOP domains
               CATH domains 1j3lB00 B:1-164  [code=3.50.30.40, no name defined]                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh...eee....ee......eeeeeeeee....hhhhhhhhh.....eeeeee..........hhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...eee..eee....eeeee..eeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3l B   1 MEARTTDLSDLYPEGEALPmVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVRSGG 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
                                              20-MSE                                                                                                                                            

Chain C from PDB  Type:PROTEIN  Length:161
 aligned with RRAAH_THET8 | Q5SIP7 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
          RRAAH_THET8     1 MEARTTDLSDLYPEGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARLAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVR 161
               SCOP domains d1j3lc_ C: Demethylmenaquinone methyltransferase                                                                                                                  SCOP domains
               CATH domains 1j3lC00 C:1-161  [code=3.50.30.40, no name defined]                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh...eee....ee......eeeeeeeee....hhhhhhhhhh.....eeeee..........hhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...eee..eee....eeeee..eeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3l C   1 MEARTTDLSDLYPEGEALPmVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVR 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
                                              20-MSE                                                                                                                                         

Chain D from PDB  Type:PROTEIN  Length:164
 aligned with RRAAH_THET8 | Q5SIP7 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
          RRAAH_THET8     1 MEARTTDLSDLYPEGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARLAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVRSGG 164
               SCOP domains d1j3ld_ D: Demethylmenaquinone methyltransferase                                                                                                                     SCOP domains
               CATH domains 1j3lD00 D:1-164  [code=3.50.30.40, no name defined]                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh...eee....ee......eeeeeeeee....hhhhhhhhhh....eeeeee..........hhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...ee....ee....eeeee..eeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3l D   1 MEARTTDLSDLYPEGEALPmVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVRSGG 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
                                              20-MSE                                                                                                                                            

Chain E from PDB  Type:PROTEIN  Length:164
 aligned with RRAAH_THET8 | Q5SIP7 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
          RRAAH_THET8     1 MEARTTDLSDLYPEGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARLAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVRSGG 164
               SCOP domains d1j3le_ E: Demethylmenaquinone methyltransferase                                                                                                                     SCOP domains
               CATH domains 1j3lE00 E:1-164  [code=3.50.30.40, no name defined]                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh...eeee...ee......eeeee..ee....hhhhhhhh......eeeeee..........hhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...............eeeee..eeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3l E   1 MEARTTDLSDLYPEGEALPmVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVRSGG 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
                                              20-MSE                                                                                                                                            

Chain F from PDB  Type:PROTEIN  Length:157
 aligned with RRAAH_THET8 | Q5SIP7 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
          RRAAH_THET8     1 MEARTTDLSDLYPEGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARLAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPP 157
               SCOP domains d1j3lf_ F: Demethylmenaquinone methyltransferase                                                                                                              SCOP domains
               CATH domains 1j3lF00 F:1-157  [code=3.50.30.40, no name defined]                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh.....eeee...ee......eeeee.eee....hhhhhhhhh.......eeee..........hhhhhhhhhhh....eeeeeee.hhhhhh.....eeeeee...........ee...ee....ee...eeeeee..eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3l F   1 MEARTTDLSDLYPEGEALPmVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPP 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
                                              20-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  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J3L)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (RRAAH_THET8 | Q5SIP7)
molecular function
    GO:0047443    4-hydroxy-4-methyl-2-oxoglutarate aldolase activity    Catalysis of the reaction: 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008948    oxaloacetate decarboxylase activity    Catalysis of the reaction: oxaloacetate = pyruvate + CO2.
    GO:0008428    ribonuclease inhibitor activity    Stops, prevents or reduces the activity of a ribonuclease, any enzyme that catalyzes the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0051252    regulation of RNA metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.

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