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(-) Description

Title :  STRUCTURE OF BACTERIAL POLYNUCLEOTIDE KINASE BOUND TO GTP AND PDNA
 
Authors :  U. Das, L. K. Wang, P. Smith, S. Shuman
Date :  15 Jun 14  (Deposition) - 08 Oct 14  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rna Repair, P-Loop Phosphotransferase, Polynucleotide Kinase, Hydrolase-Dna Complex, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Das, L. K. Wang, P. Smith, A. Munir, S. Shuman
Structures Of Bacterial Polynucleotide Kinase In A Michaeli Complex With Nucleoside Triphosphate (Ntp)-Mg2+ And 5'-Oh Rna And A Mixed Substrate-Product Complex With Ntp-Mg2+ And A 5'-Phosphorylated Oligonucleotide.
J. Bacteriol. V. 196 4285 2014
PubMed-ID: 25266383  |  Reference-DOI: 10.1128/JB.02197-14

(-) Compounds

Molecule 1 - METALLOPHOSPHOESTERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CTHE_2768
    Organism Scientific: RUMINICLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119
    Strain: ATCC 27405 / DSM 1237
 
Molecule 2 - DNA
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC POLYNUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:16 , SER A:17 , GLY A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , THR A:23 , ARG A:116 , ARG A:120 , ARG A:123 , MG A:1002 , HOH A:1101 , HOH A:1102 , HOH A:1103 , HOH A:1118 , HOH A:1124 , HOH A:1138 , HOH A:1144 , HOH A:1190 , HOH A:1214 , HOH A:1232 , DC C:1 , HOH C:112BINDING SITE FOR RESIDUE GTP A 1001
2AC2SOFTWARESER A:22 , GTP A:1001 , HOH A:1101 , HOH A:1102 , HOH A:1103BINDING SITE FOR RESIDUE MG A 1002
3AC3SOFTWARESER 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 , ARG B:123 , MG B:1002 , HOH B:1102 , HOH B:1103 , HOH B:1104 , HOH B:1142 , HOH B:1154 , HOH B:1159 , HOH B:1161 , HOH B:1221 , HOH B:1254 , HOH B:1256 , HOH B:1260BINDING SITE FOR RESIDUE GTP B 1001
4AC4SOFTWARESER B:22 , GTP B:1001 , HOH B:1102 , HOH B:1103 , HOH B:1104BINDING SITE FOR RESIDUE MG B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QM7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QM7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QM7)

(-) Exons   (0, 0)

(no "Exon" information available for 4QM7)

(-) 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
                 4qm7 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 .eeeeee..eeeeee.....hhhhhhhhhhhhh.eeehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhh..eeeee.hhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qm7 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                             


Chain C from PDB  Type:DNA  Length:4
                                    
                 4qm7 C   1 CCTG   4
   Legend:   → Mismatch (orange background)
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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 4QM7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QM7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QM7)

(-) 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 4jst 4jsy 4jt2 4jt4 4mde 4mdf 4qm6

(-) Related Entries Specified in the PDB File

4jst 4jsy 4jt2 4jt4 4mde 4mdf 4qm6