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(-) Description

Title :  HINCII BOUND TO CLEAVED, COGNATE DNA CONTAINING GTCGAC
 
Authors :  C. Etzkorn, N. C. Horton
Date :  20 Sep 04  (Deposition) - 28 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,E,F,G,H  (1x)
Biol. Unit 2:  C,D,I,J,K,L  (1x)
Keywords :  Restriction Endonuclease, Phosphoryl Transfer, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Etzkorn, N. C. Horton
Mechanistic Insights From The Structures Of Hincii Bound To Cognate Dna Cleaved From Addition Of Mg(2+) And Mn(2+)
J. Mol. Biol. V. 343 833 2004
PubMed-ID: 15476804  |  Reference-DOI: 10.1016/J.JMB.2004.08.082
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'
    Chains: E, G, I, K
    Engineered: YES
    Other Details: PHOSPHORAMIDITE SYNTHETIC CHEMISTRY
    Synthetic: YES
 
Molecule 2 - 5'-D(P*GP*AP*CP*CP*GP*G)-3'
    Chains: F, H, J, L
    Engineered: YES
    Other Details: PHOSPHORAMIDITE SYNTHETIC CHEMISTRY
    Synthetic: YES
 
Molecule 3 - TYPE II RESTRICTION ENZYME HINCII
    Chains: A, B, C, D
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HINCIIR
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: ENDONUCLEASE HINCII, R.HINCII

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): AB  EFGH    
Biological Unit 2 (1x):   CD    IJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XHU)

(-) Sites  (0, 0)

(no "Site" information available for 1XHU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XHU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XHU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XHU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XHU)

(-) Exons   (0, 0)

(no "Exon" information available for 1XHU)

(-) 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:257
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
               SCOP domains d1xhua_ A: Restriction endonuclease HincII                                                                                                                                                                                                                        SCOP domains
               CATH domains 1xhuA00 A:2-258  [code=3.40.600.10, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.....hhhhhh....hhhhhhhhh.hhhhhhhh...............eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhhh....eeeeeeeeeee.....eeeeeeeeee.hhh......ee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhu A   2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
               SCOP domains d1xhub_ B: Restriction endonuclease HincII                                                                                                                                                                                                                       SCOP domains
               CATH domains 1xhuB00 B:2-257  [code=3.40.600.10, no name defined]                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eee.hhhh.........hhhhhhhhhhhhhh...eehhhhhhhhhhhh....hhhhhhhh...hhhhhhhhh.hhhhhhh................eee.....eeeeeeeeee........eeeehhhhhhhhhhhhhhh....eeeeeeeeeeee...eeeeeeeeeee.hhh.....eee.....eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhu B   2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      


Chain C from PDB  Type:PROTEIN  Length:254
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
               SCOP domains d1xhuc_ C: Restriction endonuclease HincII                                                                                                                                                                                                                        SCOP domains
               CATH domains 1xhuC00 C:2-258  [code=3.40.600.10, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eee.hhhh..hhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhh.......hhhhhh...hhhhhhhh.....hhhhh...---..........eeee....eeeeeee...........eeeehhhhhhhhhhhh.........eeeeeeeee....eeeeeeeeeee.hhh.....eee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhu C   2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSI---FEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
                                    11        21        31        41        51        61        71        81        91       101   |   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
                                                                                                                             101 105                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:256
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
               SCOP domains d1xhud_ D: Restriction endonuclease HincII                                                                                                                                                                                                                       SCOP domains
               CATH domains 1xhuD00 D:2-257  [code=3.40.600.10, no name defined]                                                                                                                                                                                                             CATH domains
           Pfam domains (1) Endonuc-HincII-1xhuD01 D:2-257                                                                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) Endonuc-HincII-1xhuD02 D:2-257                                                                                                                                                                                                                                   Pfam domains (2)
           Pfam domains (3) Endonuc-HincII-1xhuD03 D:2-257                                                                                                                                                                                                                                   Pfam domains (3)
           Pfam domains (4) Endonuc-HincII-1xhuD04 D:2-257                                                                                                                                                                                                                                   Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhh.................hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhh................eeeee..eeeeee..eee........eeeehhhhhhhhhhhhhhh....eeeee..eeeeee..eeeeeee..ee.hhhhhhhh.ee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhu D   2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      


Chain E from PDB  Type:DNA  Length:7
                                       
                 1xhu E   1 GCCGGTC   7


Chain F from PDB  Type:DNA  Length:6
                                      
                 1xhu F   8 GACCGG  13


Chain G from PDB  Type:DNA  Length:7
                                       
                 1xhu G   1 GCCGGTC   7


Chain H from PDB  Type:DNA  Length:6
                                      
                 1xhu H   8 GACCGG  13


Chain I from PDB  Type:DNA  Length:7
                                       
                 1xhu I   1 GCCGGTC   7


Chain J from PDB  Type:DNA  Length:6
                                      
                 1xhu J   8 GACCGG  13


Chain K from PDB  Type:DNA  Length:7
                                       
                 1xhu K   1 GCCGGTC   7


Chain L from PDB  Type:DNA  Length:6
                                      
                 1xhu L   8 GACCGG  13
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Endonuc-HincII] (3)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (T2C2_HAEIF | P17743)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0009036    type II site-specific deoxyribonuclease activity    Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
biological process
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
    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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  1xhu
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  T2C2_HAEIF | P17743
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  3.1.21.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        T2C2_HAEIF | P17743: 1kc6 1tw8 1tx3 1xhv 2aud 2gie 2gig 2gih 2gii 2gij 3e3y 3e40 3e41 3e42 3e43 3e44 3e45 3ebc

(-) Related Entries Specified in the PDB File

1kc6 HINCII BOUND TO COGNATE DNA CONTAINING GTCGAC
1tw8 HINCII BOUND TO COGNATE DNA CONTAINING GTCGAC AND CA2+