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(-) Description

Title :  STRUCTURE OF RBKR (RIBOFLAVIN KINASE) FROM THERMOPLASMA ACIDOPHILUM DETERMINED IN COMPLEX WITH CTP AND ITS COGNATE DNA OPERATOR
 
Authors :  M. W. Vetting, I. A. Rodionova, X. Li, A. L. Osterman, D. A. Rodionov, S. C
Date :  26 Oct 16  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,G,H
Keywords :  Ribflavin Kinase, Marr Type Regulatory Domain, Winged-Helix-Turn- Helix Domain, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, I. A. Rodionova, X. Li, A. L. Osterman, D. A. Rodionov, S. C. Almo
Structure Of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined In Complex With Ctp And Its Cognate Dna Operator
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOFLAVIN KINASE
    Chains: A, B
    EC Number: 2.7.1.161
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23 DERIVATIVE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RIBOFLAVIN KINASE AND REGULATOR
    Gene: RIBK, TA1064
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 273075
    Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
 
Molecule 2 - DNA (5'- D(*AP*TP*TP*AP*CP*TP*AP*AP*TP*TP*CP*AP*CP*GP*AP*GP*TP*AP*A)-3')
    Chains: G
    Engineered: YES
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*TP*TP*TP*AP*CP*TP*CP*GP*TP*GP*AP*AP*TP*TP*AP*GP*TP*AP*A)-3')
    Chains: H
    Engineered: YES
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABGH

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CTP2Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2NA2Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:101 , GLY A:102 , MET A:103 , GLY A:104 , GLU A:105 , GLY A:106 , ARG A:107 , TYR A:128 , GLY A:130 , THR A:131 , LEU A:132 , ASN A:133 , LYS A:200 , TYR A:201 , LEU A:202 , ARG A:203 , NA A:302 , HOH A:408 , HOH A:431 , HOH A:444 , HOH A:450 , HOH A:451 , HOH A:482 , HOH A:496 , HOH A:498binding site for residue CTP A 301
2AC2SOFTWARETHR A:131 , ASN A:133 , CTP A:301binding site for residue NA A 302
3AC3SOFTWARESER B:101 , GLY B:102 , MET B:103 , GLY B:104 , GLU B:105 , GLY B:106 , ARG B:107 , TYR B:128 , GLY B:130 , THR B:131 , LEU B:132 , ASN B:133 , SER B:198 , LYS B:200 , TYR B:201 , LEU B:202 , ARG B:203 , NA B:302 , HOH B:401 , HOH B:405 , HOH B:407 , HOH B:414 , HOH B:441 , HOH B:449 , HOH B:450binding site for residue CTP B 301
4AC4SOFTWARETHR B:131 , ASN B:133 , CTP B:301binding site for residue NA B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TRD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5TRD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TRD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TRD)

(-) Exons   (0, 0)

(no "Exon" information available for 5TRD)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...eeeehhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhh..eee..ee....ee..eeeeeeee..eeeeeeee.......eeeee...hhhhhh......eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5trd A   5 DQYYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTEFADLSRILAIKNNVVITGTVTSGMGEGRYYVARKQYIIQFQEKLGIIPYLGTLNIKVDQASLPELRKIRGFRGIHIEGFKTEDRTFGSVKAFPAKIQNIPCFVIMPERTVYTDVIEIISDKYLREEINLHDGDRVSVEVYTEGH 223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeehhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhh..eee..ee....ee..eeeeeeee..eeeeeeee.......eeeee...hhhhhh......eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5trd B   7 YYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTEFADLSRILAIKNNVVITGTVTSGMGEGRYYVARKQYIIQFQEKLGIIPYLGTLNIKVDQASLPELRKIRGFRGIHIEGFKTEDRTFGSVKAFPAKIQNIPCFVIMPERTVYTDVIEIISDKYLREEINLHDGDRVSVEVYTE 221
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216     


Chain G from PDB  Type:DNA  Length:19
                                                   
                 5trd G   1 ATTACTAATTCACGAGTAA  19
                                    10         


Chain H from PDB  Type:DNA  Length:19
                                                   
                 5trd H   1 TTTACTCGTGAATTAGTAA  19
                                    10
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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 5TRD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TRD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TRD)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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