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(-) Description

Title :  STRUCTURE OF CLOSTRIDIUM THERMOCELLUM POLYNUCLEOTIDE KINASE BOUND TO UTP
 
Authors :  U. Das, L. K. Wang, P. Smith, S. Shuman
Date :  22 Mar 13  (Deposition) - 28 Aug 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna Repair, P-Loop Phosphotransferase, Polynucleotide Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Das, L. K. Wang, P. Smith, S. Shuman
Structural And Biochemical Analysis Of The Phosphate Donor Specificity Of The Polynucleotide Kinase Component Of The Bacterial Pnkphen1 Rna Repair System.
Biochemistry V. 52 4734 2013
PubMed-ID: 23721485  |  Reference-DOI: 10.1021/BI400412X

(-) Compounds

Molecule 1 - METALLOPHOSPHOESTERASE
    Chains: A, B
    EC Number: 2.7.1.78
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CTHE_2768
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119
    Strain: ATCC 27405 / DSM 1237

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4UTP2Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:22 , UTP A:202 , HOH A:306 , HOH A:308 , HOH A:316BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWARESER A:16 , SER A:17 , GLY A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , THR A:23 , ASP A:38 , ARG A:116 , ARG A:120 , ARG A:123 , MG A:201 , HOH A:306 , HOH A:308 , HOH A:316 , HOH A:321 , HOH A:363 , HOH A:369 , HOH A:410 , HOH A:426 , HOH A:432BINDING SITE FOR RESIDUE UTP A 202
3AC3SOFTWARESER B:22 , UTP B:202 , HOH B:301 , HOH B:302 , HOH B:303BINDING SITE FOR RESIDUE MG B 201
4AC4SOFTWARESER B:16 , SER B:17 , GLY B:18 , SER B:19 , GLY B:20 , LYS B:21 , SER B:22 , THR B:23 , ARG B:116 , ARG B:120 , MG B:201 , HOH B:301 , HOH B:302 , HOH B:303 , HOH B:329 , HOH B:332 , HOH B:335 , HOH B:347 , HOH B:350 , HOH B:361 , HOH B:376 , HOH B:399BINDING SITE FOR RESIDUE UTP B 202
5AC5SOFTWAREPHE B:24 , HOH B:317 , HOH B:391 , HOH B:405 , HOH B:428BINDING SITE FOR RESIDUE NA B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JST)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JST)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JST)

(-) Exons   (0, 0)

(no "Exon" information available for 4JST)

(-) 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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee.....hhhhhhhhhhhhh.eeehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhh..eeeee.hhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jst A   0 SmKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLmSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEIAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQmKKSIKGLQREGFRYVYILNSPEEVEEVVFERQP 170
                             |       9        19        29        39    |   49        59        69        79        89        99       109       119       129       139       149       159       169 
                             |                                         44-MSE                                                                                      137-MSE                             
                             1-MSE                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....eeeeee.....hhhhhhhhhhhhh.eeehhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhh..eeeee.hhhhhhheeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jst B   0 SmKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLmSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEIAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQmKKSIKGLQREGFRYVYILNSPEEVEEVVFERQP 170
                             |       9        19        29        39    |   49        59        69        79        89        99       109       119       129       139       149       159       169 
                             1-MSE                                     44-MSE                                                                                      137-MSE
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  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  (0, 0)

(no "SCOP Domain" information available for 4JST)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JST)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JST)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        A3DJ38_CLOTH | A3DJ38: 3ty5 3ty8 3ty9 4drf 4e6n 4gp6 4gp7 4j6o 4jsy 4jt2 4jt4 4mde 4mdf 4qm6 4qm7

(-) Related Entries Specified in the PDB File

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4gp7 SAME PROTEIN COMPLEXED WITH ATP
4jsy
4jt2
4jt4