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(-) Description

Title :  CRYSTAL STRUCTURE OF APO NOTI RESTRICTION ENDONUCLEASE
 
Authors :  A. R. Lambert, D. Sussman, B. Shen, B. L. Stoddard
Date :  07 Jan 08  (Deposition) - 22 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Restriction Enzyme Fold, Pd-(D/E)-Xk, Restriction Endonuclease, Rare- Cutting, Fe-Cys4 Motif, Iron-Sulfur Protein, Hydrolase (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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:42 , CYS A:55 , CYS A:65 , CYS A:81BINDING SITE FOR RESIDUE FE A 901
2AC2SOFTWARECYS B:42 , CYS B:55 , CYS B:65 , CYS B:81BINDING SITE FOR RESIDUE FE B 902
3AC3SOFTWAREGLU A:156 , PHE A:157 , SER A:158 , LYS A:245 , LYS B:236BINDING SITE FOR RESIDUE SO4 A 801
4AC4SOFTWARELYS A:236 , GLU B:156 , PHE B:157 , SER B:158 , GLN B:241 , LYS B:245BINDING SITE FOR RESIDUE SO4 B 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BVQ)

(-) 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:342
 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 ..eeee............hhhhhhhhhhh.hhhhhhhh........hhhhh...eeee.----.eeee.hhhhhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhhh..eeeeeee.......ee........ee..eeeeeeee.....eeeeeeeeee........hhhhhhhhhhhhh..-------.hhhhhhhhhh.............hhhhhhhhhhh.....eeeeeeeeehhhhhhhhhhh.....ee.....eee.........eeeeeee............eeeeeeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bvq A  12 ANFIAEFFGHRVYPEVVSTEAARNDQATGTCPFLTAAKLVETSCVKAETSRGVCVVNTA----RYDWLVCPNRALDPLFmSAASRKLFGYGPTEPLQFIAAPTLADQAVRDGIREWLDRGVHVVAYFQEKLGGELSISKTDSSPEFSFDWTLAEVESIYPVPKIKRYGVLEIQTmDFHGSYKHAVGAIDIALVEG-------PTPAGRAALSKKmEGPNLSNVFKRTFYQmAYKFALSGHQRCAGTGFAIPQSVWKSWLRHLANPTLIDNGDGTFSLGDTRNDSENAWIFVFELDPDTDASPRPLAPHLEIRVNVDTLIDLALRESPRAALGPSGPVATFTDKVEARmLRFWP 364
                                    21        31        41        51        61        |-   |    81        91       101       111       121       131       141       151       161       171       181    |  191       201    |    -  |    221    |  231       241|      251       261       271       281       291       301       311       321       331       341       351       361   
                                                                                     70   75              91-MSE                                                                                        186-MSE             206     214         226-MSE         242-MSE                                                                                                              359-MSE 


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with Q2I6W2_9NOCA | Q2I6W2 from UniProtKB/TrEMBL  Length:383

    Alignment length:355
                                    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 ANFIAEFFGHRVYPEVVSTEAARNDQATGTCPFLTAAKLVETSCVKAETSRGVCVVNTAVDNERYDWLVCPNRALDPLFMSAASRKLFGYGPTEPLQFIAAPTLADQAVRDGIREWLDRGVHVVAYFQEKLGGELSISKTDSSPEFSFDWTLAEVESIYPVPKIKRYGVLEIQTMDFHGSYKHAVGAIDIALVEGIDFHGWLPTPAGRAALSKKMEGPNLSNVFKRTFYQMAYKFALSGHQRCAGTGFAIPQSVWKSWLRHLANPTLIDNGDGTFSLGDTRNDSENAWIFVFELDPDTDASPRPLAPHLEIRVNVDTLIDLALRESPRAALGPSGPVATFTDKVEARMLRFWPKT 366
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..ee.......hhhhhhhhhhh.hhhhhhhh..............eeeeee......eeee.hhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhh.eeeeee.......eee........eee.eeeeeeee.....eeeeeeeeee........hhhhhhhhhhhhhh...---....hhhhhhhh......hhhhh...hhhhhhhhhhh.....eeeeeeeeehhhhhhhhhhh........................eeeeeee............eeeeeee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bvq B  12 ANFIAEFFGHRVYPEVVSTEAARNDQATGTCPFLTAAKLVETSCVKAETSRGVCVVNTAVDNERYDWLVCPNRALDPLFmSAASRKLFGYGPTEPLQFIAAPTLADQAVRDGIREWLDRGVHVVAYFQEKLGGELSISKTDSSPEFSFDWTLAEVESIYPVPKIKRYGVLEIQTmDFHGSYKHAVGAIDIALVEGID---WLPTPAGRAALSKKmEGPNLSNVFKRTFYQmAYKFALSGHQRCAGTGFAIPQSVWKSWLRHLANPTLIDNGDGTFSLGDTRNDSENAWIFVFELDPDTDASPRPLAPHLEIRVNVDTLIDLALRESPRAALGPSGPVATFTDKVEARmLRFWPKT 366
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181    |  191       201      |  -|      221    |  231       241|      251       261       271       281       291       301       311       321       331       341       351       361     
                                                                                                          91-MSE                                                                                        186-MSE               208 212           226-MSE         242-MSE                                                                                                              359-MSE
   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 3BVQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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

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        Q2I6W2_9NOCA | Q2I6W2: 3c25

(-) Related Entries Specified in the PDB File

3bvr