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(-) Description

Title :  CRYSTAL STRUCTURE OF BACTERIAL PNKP-C/HEN1-N HETERODIMER
 
Authors :  R. H. Huang, P. Wang
Date :  17 Feb 12  (Deposition) - 01 Aug 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rna Repair, Rna Ligase, Ligase-Activating, Protein Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Wang, C. M. Chan, D. Christensen, C. Zhang, K. Selvadurai, R. H. Huan
Molecular Basis Of Bacterial Protein Hen1 Activating The Ligase Activity Of Bacterial Protein Pnkp For Rna Repair.
Proc. Natl. Acad. Sci. Usa V. 109 13248 2012
PubMed-ID: 22847431  |  Reference-DOI: 10.1073/PNAS.1209805109

(-) Compounds

Molecule 1 - METALLOPHOSPHOESTERASE
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINAL HALF OF BACTERIAL PNKP
    Gene: CTHE_2768
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119
    Strain: ATCC 27405 / DSM 1237
 
Molecule 2 - METHYLTRANSFERASE TYPE 12
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL HALF OF BACTERIAL HEN1
    Gene: CTHE_2767
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119
    Strain: ATCC 27405 / DSM 1237

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:716 , PHE B:206 , GLY B:209 , GLU B:210 , GLY B:211 , LEU B:213 , VAL B:214BINDING SITE FOR RESIDUE GOL B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:609 -Pro A:610
2Ser A:766 -Gly A:767
3Met C:609 -Pro C:610
4Ser C:766 -Gly C:767

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DRF)

(-) 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:408
 aligned with A3DJ38_CLOTH | A3DJ38 from UniProtKB/TrEMBL  Length:870

    Alignment length:419
                                   461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861         
         A3DJ38_CLOTH   452 LGKKIITTRLMSSITIHEENSIAALEVMSRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQKLLEEQYSAVGISGRVVLDEAVKLLKQASLNKTVSFDVSRQTSGKNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......eeehhhhhhhhhhhhhh...............ee...........hhhhhhhhhhh....eeeeeee...eeeeeeee.hhhhhhhhh.......eeeee........hhhhhhhhhhhhhhhhhh.hhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------.ee.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhheeeeeeeeee..ee....hhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhhhhh.....eeeeee.....ee..ee....eeee....hhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4drf A 452 LGKKIITTRLMSSITIHEENSIAALEVMSRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQKLLEEQYSAVGISGRVVLDEAVKLLKQASLNK-----------GKNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
                                   461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641      |  -       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861         
                                                                                                                                                                                                                              648         660                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with A3DJ37_CLOTH | A3DJ37 from UniProtKB/TrEMBL  Length:465

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         A3DJ37_CLOTH     1 MILTITYTQPPATDLGYLLHKNPSRPQTFELNHGKAHIFYPEATSERCTVALLLDIDPIDLARGKKGSSGEGGLFDYVNDRPYVSSSFMSVAISRVFGTAMSGKCKEKPELAAIKLPLKAKIMMLPCKGGEEIIYRLFEPLGYKVDVEGYMLDEKFPEWGKSRYYTVSLEGEVRVRDLLNHIYVLIPVLDSEKHYWVGEDEIDKLFQHGEGWLVDHPEKELIT 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhh......eeeee..eeeeeeeeee....eeeeeeeee.....-----------hhhhh..hhhhh.hhhhhhhhhhhhhhhhhh......hhhhh.eeeeeeeeeee..hhhhhhhhhhhhhh.eeeeeeee....hhhh.eeeeeeeeeeeeehhhhhhhhhhhhhhhhh.hhhhh------...............hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4drf B   1 MILTITYTQPPATDLGYLLHKNPSRPQTFELNHGKAHIFYPEATSERCTVALLLDIDPIDL-----------GLFDYVNDRPYVSSSFMSVAISRVFGTAMSGKCKEKPELAAIKLPLKAKIMMLPCKGGEEIIYRLFEPLGYKVDVEGYMLDEKFPEWGKSRYYTVSLEGEVRVRDLLNHIYVLIPVLDSEKHYW------DKLFQHGEGWLVDHPEKELIT 223
                                    10        20        30        40        50        60|        -  |     80        90       100       110       120       130       140       150       160       170       180       190     |   -  |    210       220   
                                                                                       61          73                                                                                                                        196    203                    


Chain C from PDB  Type:PROTEIN  Length:408
 aligned with A3DJ38_CLOTH | A3DJ38 from UniProtKB/TrEMBL  Length:870

    Alignment length:419
                                   461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861         
         A3DJ38_CLOTH   452 LGKKIITTRLMSSITIHEENSIAALEVMSRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQKLLEEQYSAVGISGRVVLDEAVKLLKQASLNKTVSFDVSRQTSGKNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......eeehhhhhhhhhhhhhh...............ee...........hhhhhhhhhhh....eeeeeee...eeeeeeee.hhhhhhhhh.......eeeee........hhhhhhhhhhhhhhhhhh.hhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------.ee.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhheeeeeeeeee..ee....hhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhhhhh.....eeeeee.....ee..ee....eeee....hhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4drf C 452 LGKKIITTRLMSSITIHEENSIAALEVMSRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQKLLEEQYSAVGISGRVVLDEAVKLLKQASLNK-----------GKNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
                                   461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641      |  -       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861         
                                                                                                                                                                                                                              648         660                                                                                                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:206
 aligned with A3DJ37_CLOTH | A3DJ37 from UniProtKB/TrEMBL  Length:465

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         A3DJ37_CLOTH     1 MILTITYTQPPATDLGYLLHKNPSRPQTFELNHGKAHIFYPEATSERCTVALLLDIDPIDLARGKKGSSGEGGLFDYVNDRPYVSSSFMSVAISRVFGTAMSGKCKEKPELAAIKLPLKAKIMMLPCKGGEEIIYRLFEPLGYKVDVEGYMLDEKFPEWGKSRYYTVSLEGEVRVRDLLNHIYVLIPVLDSEKHYWVGEDEIDKLFQHGEGWLVDHPEKELIT 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhh......eeeee..eeeeeeeeee....eeeeeeeee.....-----------hhhhh..hhhhh.hhhhhhhhhhhhhhhhhh......hhhhh.eeeeeeeeeee..hhhhhhhhhhhhhh.eeeeeeee....hhhh.eeeeeeeeeeeeehhhhhhhhhhhhhhhhh.hhhhh------...............hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4drf D   1 MILTITYTQPPATDLGYLLHKNPSRPQTFELNHGKAHIFYPEATSERCTVALLLDIDPIDL-----------GLFDYVNDRPYVSSSFMSVAISRVFGTAMSGKCKEKPELAAIKLPLKAKIMMLPCKGGEEIIYRLFEPLGYKVDVEGYMLDEKFPEWGKSRYYTVSLEGEVRVRDLLNHIYVLIPVLDSEKHYW------DKLFQHGEGWLVDHPEKELIT 223
                                    10        20        30        40        50        60|        -  |     80        90       100       110       120       130       140       150       160       170       180       190     |   -  |    210       220   
                                                                                       61          73                                                                                                                        196    203
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (A3DJ38_CLOTH | A3DJ38)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Chain B,D   (A3DJ37_CLOTH | A3DJ37)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0008173    RNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0001510    RNA methylation    Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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 Related Entries

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

UniProtKB/TrEMBL
        A3DJ37_CLOTH | A3DJ37: 3jwg 3jwi 4dqz 4e6n
        A3DJ38_CLOTH | A3DJ38: 3ty5 3ty8 3ty9 4e6n 4gp6 4gp7 4j6o 4jst 4jsy 4jt2 4jt4 4mde 4mdf 4qm6 4qm7

(-) Related Entries Specified in the PDB File

4dqz