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(-) Description

Title :  CRYSTAL STRUCTURE OF NOTI RESTRICTION ENDONUCLEASE BOUND TO COGNATE DNA
 
Authors :  A. R. Lambert, D. Sussman, B. Shen, B. L. Stoddard
Date :  24 Jan 08  (Deposition) - 12 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Restriction Enzyme Fold, Pd-(D/E)-Xk, Restriction Endonuclease, Rare-Cutting, Fe-Cys4 Motif, Iron-Sulfur Protein, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Lambert, D. Sussman, B. Shen, R. Maunus, J. Nix, J. Samuelson, S. Y. Xu, B. L. Stoddard
Structures Of The Rare-Cutting Restriction Endonuclease Not Reveal A Unique Metal Binding Fold Involved In Dna Binding.
Structure V. 16 558 2008
PubMed-ID: 18400177  |  Reference-DOI: 10.1016/J.STR.2008.01.017

(-) Compounds

Molecule 1 - NOTI RESTRICTION ENDONUCLEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NOTIR
    Organism Scientific: NOCARDIA OTITIDISCAVIARUM
    Organism Taxid: 1823
 
Molecule 2 - DNA (5'- D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DC P*DCP*DGP*DCP*DCP*DG)-3')
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC DNA CONSTRUCT CONTAINING COGNATE RECOGNITION SEQUENCE OF NOTI
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DC P*DCP*DTP*DCP*DCP*DG)-3')
    Chains: D
    Engineered: YES
    Other Details: SYNTHETIC DNA CONSTRUCT CONTAINING COGNATE RECOGNITION SEQUENCE OF NOTI
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2FE2Ligand/IonFE (III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:145 , ASP A:160 , HOH A:946BINDING SITE FOR RESIDUE CA A 801
2AC2SOFTWAREGLU A:182 , DG D:10 , HOH A:923BINDING SITE FOR RESIDUE CA A 802
3AC3SOFTWAREGLU B:145 , ASP B:160 , DC C:9BINDING SITE FOR RESIDUE CA B 803
4AC4SOFTWAREGLU B:182 , HOH B:918BINDING SITE FOR RESIDUE CA B 804
5AC5SOFTWARECYS A:42 , CYS A:55 , CYS A:65 , CYS A:81BINDING SITE FOR RESIDUE FE A 901
6AC6SOFTWARECYS B:42 , CYS B:55 , CYS B:65 , CYS B:81BINDING SITE FOR RESIDUE FE B 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C25)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C25)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C25)

(-) Exons   (0, 0)

(no "Exon" information available for 3C25)

(-) 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:354
 aligned with Q2I6W2_9NOCA | Q2I6W2 from UniProtKB/TrEMBL  Length:383

    Alignment length:354
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
         Q2I6W2_9NOCA    12 ANFIAEFFGHRVYPEVVSTEAARNDQATGTCPFLTAAKLVETSCVKAETSRGVCVVNTAVDNERYDWLVCPNRALDPLFMSAASRKLFGYGPTEPLQFIAAPTLADQAVRDGIREWLDRGVHVVAYFQEKLGGELSISKTDSSPEFSFDWTLAEVESIYPVPKIKRYGVLEIQTMDFHGSYKHAVGAIDIALVEGIDFHGWLPTPAGRAALSKKMEGPNLSNVFKRTFYQMAYKFALSGHQRCAGTGFAIPQSVWKSWLRHLANPTLIDNGDGTFSLGDTRNDSENAWIFVFELDPDTDASPRPLAPHLEIRVNVDTLIDLALRESPRAALGPSGPVATFTDKVEARMLRFWPK 365
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee............hhhhhhhhh...hhhhhhh...............eeeeeee..eeeeee..hhhh..hhhhhhhhhhhh.......eeeeehhhhh.hhhhhhhhhhhhh..eeeeee.......eee........eee.eeeeeeee.....eeeeeeeeeee.......hhhhhhhhhhhhhh..........hhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhh............eee.........eeeeeeee..........eeeeeeeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c25 A  12 ANFIAEFFGHRVYPEVVSTEAARNDQATGTCPFLTAAKLVETSCVKAETSRGVCVVNTAVDNERYDWLVCPNRALDPLFMSAASRKLFGYGPTEPLQFIAAPTLADQAVRDGIREWLDRGVHVVAYFQEKLGGELSISKTDSSPEFSFDWTLAEVESIYPVPKIKRYGVLEIQTMDFHGSYKHAVGAIDIALVEGIDFHGWLPTPAGRAALSKKMEGPNLSNVFKRTFYQMAYKFALSGHQRCAGTGFAIPQSVWKSWLRHLANPTLIDNGDGTFSLGDTRNDSENAWIFVFELDPDTDASPRPLAPHLEIRVNVDTLIDLALRESPRAALGPSGPVATFTDKVEARMLRFWPK 365
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    


Chain B from PDB  Type:PROTEIN  Length:353
 aligned with Q2I6W2_9NOCA | Q2I6W2 from UniProtKB/TrEMBL  Length:383

    Alignment length:353
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   
         Q2I6W2_9NOCA    12 ANFIAEFFGHRVYPEVVSTEAARNDQATGTCPFLTAAKLVETSCVKAETSRGVCVVNTAVDNERYDWLVCPNRALDPLFMSAASRKLFGYGPTEPLQFIAAPTLADQAVRDGIREWLDRGVHVVAYFQEKLGGELSISKTDSSPEFSFDWTLAEVESIYPVPKIKRYGVLEIQTMDFHGSYKHAVGAIDIALVEGIDFHGWLPTPAGRAALSKKMEGPNLSNVFKRTFYQMAYKFALSGHQRCAGTGFAIPQSVWKSWLRHLANPTLIDNGDGTFSLGDTRNDSENAWIFVFELDPDTDASPRPLAPHLEIRVNVDTLIDLALRESPRAALGPSGPVATFTDKVEARMLRFWP 364
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee............hhhhhhhhh...hhhhhhh...............eeeeeee..eeeeee..hhhh..hhhhhhhhhhhh.......eeeeehhhhh.hhhhhhhhhhhhh..eeeeee.......eee........eee.eeeeeeee.....eeeeeeeeeee.......hhhhhhhhhhhhhh..........hhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhh............eee.........eeeeeeee..........eeeeeeeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c25 B  12 ANFIAEFFGHRVYPEVVSTEAARNDQATGTCPFLTAAKLVETSCVKAETSRGVCVVNTAVDNERYDWLVCPNRALDPLFMSAASRKLFGYGPTEPLQFIAAPTLADQAVRDGIREWLDRGVHVVAYFQEKLGGELSISKTDSSPEFSFDWTLAEVESIYPVPKIKRYGVLEIQTMDFHGSYKHAVGAIDIALVEGIDFHGWLPTPAGRAALSKKMEGPNLSNVFKRTFYQMAYKFALSGHQRCAGTGFAIPQSVWKSWLRHLANPTLIDNGDGTFSLGDTRNDSENAWIFVFELDPDTDASPRPLAPHLEIRVNVDTLIDLALRESPRAALGPSGPVATFTDKVEARMLRFWP 364
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   


Chain C from PDB  Type:DNA  Length:22
                                                      
                 3c25 C   1 CGGAGGCGCGGCCGCGCCGCCG  22
                                    10        20  


Chain D from PDB  Type:DNA  Length:22
                                                      
                 3c25 D   1 CGGCGGCGCGGCCGCGCCTCCG  22
                                    10        20
   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 3C25)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3C25)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C25)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q2I6W2_9NOCA | Q2I6W2)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/TrEMBL
        Q2I6W2_9NOCA | Q2I6W2: 3bvq

(-) Related Entries Specified in the PDB File

3bvq CRYSTAL STRUCTURE OF APO NOTI RESTRICTION ENDONUCLEASE