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(-) Description

Title :  STRUCTURE OF BACTERIAL POLYNUCLEOTIDE KINASE MICHAELIS COMPLEX BOUND TO GTP AND DNA
 
Authors :  S. Shuman, U. Das, L. K. Wang, P. Smith, A. Jacewicz
Date :  22 Aug 13  (Deposition) - 06 Nov 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rna Repair, P-Loop Phosphotransferase, Transferase, Hydrolase-Dna Complex, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Das, L. K. Wang, P. Smith, A. Jacewicz, S. Shuman
Structures Of Bacterial Polynucleotide Kinase In A Michaeli Complex With Gtp*Mg2+ And 5'-Oh Oligonucleotide And A Product Complex With Gdp*Mg2+ And 5'-Po4 Oligonucleotide Reveal A Mechanism Of General Acid-Base Catalysis And The Determinants Of Phosphoacceptor Recognition.
Nucleic Acids Res. V. 42 1152 2014
PubMed-ID: 24150947  |  Reference-DOI: 10.1093/NAR/GKT936

(-) Compounds

Molecule 1 - METALLOPHOSPHOESTERASE
    Chains: A, B
    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
 
Molecule 2 - DNA (5'-D(*CP*CP*TP*GP*T)-3')
    Chains: C, D
    Engineered: YES
    Other Details: OBTAINED FROM COMMERCIAL SYNTHETIC SOURCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
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 , ASN A:38 , ARG A:116 , ARG A:120 , ARG A:123 , MG A:1002 , HOH A:1101 , HOH A:1102 , HOH A:1103 , HOH A:1155 , HOH A:1156 , HOH A:1186 , HOH A:1211 , DC C:1BINDING 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
3AC3SOFTWAREHIS A:62 , TYR A:63 , SER A:66 , GLU A:92 , ILE A:93 , HOH A:1151 , HOH A:1167 , HOH A:1231 , HOH A:1243 , HOH A:1271 , DG C:4 , DT C:5BINDING SITE FOR RESIDUE CIT A 1003
4AC4SOFTWARESER B:16 , SER B:17 , GLY B:18 , SER B:19 , GLY B:20 , LYS B:21 , SER B:22 , THR B:23 , ASN B:38 , ARG B:116 , ARG B:120 , ARG B:123 , MG B:1002 , HOH B:1101 , HOH B:1102 , HOH B:1103 , HOH B:1149 , HOH B:1169 , HOH B:1197 , HOH B:1200 , DC D:1BINDING SITE FOR RESIDUE GTP B 1001
5AC5SOFTWARESER B:22 , GTP B:1001 , HOH B:1101 , HOH B:1102 , HOH B:1103BINDING SITE FOR RESIDUE MG B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MDF)

(-) 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    
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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.eeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhh..eeeee.hhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdf A   0 SMKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSNFCRGLVSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEIAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQMKKSIKGLQREGFRYVYILNSPEEVEEVVFERQP 170
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 


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.eeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhh..eeeee.hhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdf B   0 SMKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSNFCRGLVSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEIAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQMKKSIKGLQREGFRYVYILNSPEEVEEVVFERQP 170
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 


Chain C from PDB  Type:DNA  Length:5
                                     
                 4mdf C   1 CCTGT   5


Chain D from PDB  Type:DNA  Length:5
                                     
                 4mdf D   1 CCTGT   5
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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 4MDF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4gp6 4gp7 4jst 4jsy 4jt2 4jt4 4mde