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(-) Description

Title :  CRYSTAL STRUCTURE OF BACTERIAL PNKP-C/HEN1-N HETERODIMER
 
Authors :  R. H. Huang, P. Wang
Date :  15 Mar 12  (Deposition) - 01 Aug 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
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
    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
    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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREAMP A:902 , HOH A:1058 , HOH A:1059 , HOH A:1060 , HOH A:1061 , HOH A:1100BINDING SITE FOR RESIDUE MG A 901
2AC2SOFTWAREGLU A:529 , GLN A:530 , LYS A:531 , HIS A:532 , ARG A:536 , GLU A:607 , PHE A:704 , GLU A:769 , LYS A:774 , LYS A:792 , MG A:901 , HOH A:1058 , HOH A:1069 , HOH A:1089 , HOH A:1101BINDING SITE FOR RESIDUE AMP A 902
3AC3SOFTWAREAMP C:902 , HOH C:1063 , HOH C:1064 , HOH C:1065 , HOH C:1066 , HOH C:1109BINDING SITE FOR RESIDUE MG C 901
4AC4SOFTWAREGLU C:529 , GLN C:530 , LYS C:531 , HIS C:532 , ARG C:536 , GLU C:607 , PHE C:704 , GLU C:769 , LYS C:774 , LYS C:792 , MG C:901 , HOH C:1040 , HOH C:1064 , HOH C:1078BINDING SITE FOR RESIDUE AMP C 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E6N)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:609 -Pro A:610
2Pro B:10 -Pro B:11
3Met C:609 -Pro C:610
4Pro D:10 -Pro D:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E6N)

(-) Exons   (0, 0)

(no "Exon" information available for 4E6N)

(-) 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:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.......eeehhhhhhhhhhhhhhh..............ee...........hhhhhhhhhhh....eeeeee....eeeeeeee.hhhhhhhhhh......eeee.........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhheeeeeeeeee..ee....hhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhhhhhhh...eeeeee.....ee..ee....eeee....hhhhhh....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e6n A 453 GKKIITTRLMSSITIHEENSIAALEVMSRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQKLLEEQYSAVGISGRVVLDEAVKLLKQASLNKGKNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
                                   462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642     ||663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       
                                                                                                                                                                                                                             648|                                                                                                                                                                                                                  
                                                                                                                                                                                                                              660                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhh.......eeeee..eeeeeeeeee....eeeeeeeeehhhhhhhh.hhhhh.hhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhh.eeeeeeeeeee...hhhhhhhhhhhhh.eeeeeeee....hhhh.eeeeeeeeeeeeehhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e6n B   1 MILTITYTQPPATDLGYLLHKNPSRPQTFELNHGKAHIFYPEATSERCTVALLLDIDPIDLARGGLFDYVNDRPYVSSSFMSVAISRVFGTAMSGKCKEKPELAAIKLPLKAKIMMLPCKGGEEIIYRLFEPLGYKVDVEGYMLDEKFPEWGKSRYYTVSLEGEVRVRDLLNHIYVLIPVLDSEKHYWVGEDEIDKLFQHGEGWLVDHPEKELITGRY 226
                                    10        20        30        40        50        60   ||   78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
                                                                                          64|                                                                                                                                                         
                                                                                           73                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.......eeehhhhhhhhhhhhhhh..............ee...........hhhhhhhhhhh....eeeeee....eeeeeeee.hhhhhhhhhh......eeee.........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhheeeeeeeeee..ee.hhhhhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhhhhhhh...eeeeee.....ee..ee....eeee....hhhhhh....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e6n C 453 GKKIITTRLMSSITIHEENSIAALEVMSRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQKLLEEQYSAVGISGRVVLDEAVKLLKQASLNKGKNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
                                   462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642     ||663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       
                                                                                                                                                                                                                             648|                                                                                                                                                                                                                  
                                                                                                                                                                                                                              660                                                                                                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhh......eeeee..eeeeeeeeee....eeeeeeeeehhhhhhhh.hhhhh.hhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhh.eeeeeeeeeee...hhhhhhhhhhhhh.eeeeeeee....hhhh.eeeeeeeeeeeeehhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e6n D   1 MILTITYTQPPATDLGYLLHKNPSRPQTFELNHGKAHIFYPEATSERCTVALLLDIDPIDLARGGLFDYVNDRPYVSSSFMSVAISRVFGTAMSGKCKEKPELAAIKLPLKAKIMMLPCKGGEEIIYRLFEPLGYKVDVEGYMLDEKFPEWGKSRYYTVSLEGEVRVRDLLNHIYVLIPVLDSEKHYWVGEDEIDKLFQHGEGWLVDHPEKELITGRY 226
                                    10        20        30        40        50        60   ||   78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
                                                                                          64|                                                                                                                                                         
                                                                                           73
   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 4E6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E6N)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4E6N)