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(-) Description

Title :  CRYSTAL STRUCTURE OF C. THERMOCELLUM PNKP LIGASE DOMAIN IN COMPLEX WITH ATP
 
Authors :  P. Smith, L. Wang, S. Shuman
Date :  23 Sep 11  (Deposition) - 25 Jan 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Ligase/Mrna Capping Enzyme, Rna Ligase, Adenylyltransferase, Hen1, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Smith, L. K. Wang, P. A. Nair, S. Shuman
The Adenylyltransferase Domain Of Bacterial Pnkp Defines A Unique Rna Ligase Family.
Proc. Natl. Acad. Sci. Usa V. 109 2296 2012
PubMed-ID: 22308407  |  Reference-DOI: 10.1073/PNAS.1116827109

(-) Compounds

Molecule 1 - POLYNUCLEOTIDE 2',3'-CYCLIC PHOSPHATE PHOSPHODIESTERASE / POLYNUCLEOTIDE 5'-HYDROXYL-KINASE / POLYNUCLEOTIDE 3'-PHOSPHATASE
    Chains: A, B
    EC Number: 6.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: NUCLEOTIDE LIGASE
    Gene: CTHE_2768
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119
    Strain: ATCC 27405

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:51 , HOH A:139 , HOH A:199 , HOH A:208 , HOH A:212 , GLN A:530 , LYS A:531 , SER A:535 , ARG A:536 , ARG A:565 , GLU A:607 , PHE A:704 , LYS A:774 , LYS A:792 , LYS B:639BINDING SITE FOR RESIDUE ATP A 1001
2AC2SOFTWAREHOH B:17 , HOH B:118 , HOH B:127 , THR B:495 , MET B:496 , LYS B:531 , ARG B:536 , ARG B:565 , GLU B:607 , PHE B:704 , LYS B:774 , LYS B:792 , LYS B:824 , LEU B:870BINDING SITE FOR RESIDUE ADP B 1001
3AC3SOFTWAREHOH B:75 , HOH B:168 , TYR B:491 , LEU B:492 , PRO B:494 , MET B:496 , ALA B:790 , GLU B:831 , PHE B:832 , GLY B:835 , MET B:836BINDING SITE FOR RESIDUE PGE B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TY5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:814 -Arg A:815
2Met B:609 -Pro B:610

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TY5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TY5)

(-) Exons   (0, 0)

(no "Exon" information available for 3TY5)

(-) 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:381
 aligned with A3DJ38_CLOTH | A3DJ38 from UniProtKB/TrEMBL  Length:870

    Alignment length:394
                                   486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866    
         A3DJ38_CLOTH   477 EVMSRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQKLLEEQYSAVGISGRVVLDEAVKLLKQASLNKTVSFDVSRQTSGKNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.......ee...........hhhhhhhhhhh....eeeeee....eeeeeeee.hhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....eehhhhhhh....hhhhhhhhhhhhhhhh..-------------...hhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhh.eeeeeeeeeee..ee....hhhhhhhhhhhhh...........eeeee..hhhhhhhhhhhhhhhhhh...eeeeee.....ee..ee....eeee...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ty5 A 477 RHMSRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCGQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQKLLEEQYSAVGISGRVVLDEAVKLLKQASLN-------------KNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
                                   486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646|        -    |  666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866    
                                                                                                                                                                                                    647           661                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:381
 aligned with A3DJ38_CLOTH | A3DJ38 from UniProtKB/TrEMBL  Length:870

    Alignment length:391
                                   489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869 
         A3DJ38_CLOTH   480 SRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQKLLEEQYSAVGISGRVVLDEAVKLLKQASLNKTVSFDVSRQTSGKNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................ee...........hhhhhhhhhhh....eeeeee....eeeeeeee.hhhhhhhhhh......eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh...---........hhhhhhhhhhhhhhhhhh.....-------.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhheeeeeeeeee..ee....hhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhhhhh.....eeeeee.....ee..ee....eeeehhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ty5 B 480 SRFAADPHWLIYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCGQKHMGSRAVVIVCKDSQVAEKRFGVLDGTAGICYTRTGRHFFDDMQLEAELIDRVRKVLDKSGFWGDFNTDWVCLDCELMPWSAKAQK---EQYSAVGISGRVVLDEAVKLLKQASLNKTVS-------SGKNADINELLQRFTERSEMMQKYVEAYRKYCWPVNSIDDLKLAPFHILATEGKVHSDKNHIWHMDTIAKYCTQDDSLIMATNHILVDVTDAESVDKGIKWWEDLTASGGEGMVVKPYDFIVKNGRELLQPAVKCRGREYLRIIYGPEYTMDENIERLRNRAVGKKRSLALREFSLGMEALERFVRNEPLYRVHECVFGVLALESEPVDPRL 870
                                   489       499       509       519       529       539       549       559       569       579       589       599       609       | - |     629       639       649 |     659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869 
                                                                                                                                                                   617 621                           651     659
   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 3TY5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TY5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TY5)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

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  3ty5
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  6.5.1.3
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 Related Entries

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

UniProtKB/TrEMBL
        A3DJ38_CLOTH | A3DJ38: 3ty8 3ty9 4drf 4e6n 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 3TY5)