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(-) Description

Title :  CRYSTAL STRUCTURAL ANALYSIS OF HINDIII RESTRICTION ENDONUCLEASE IN COMPLEX WITH COGNATE DNA AT 2.0 ANGSTROM RESOLUTION
 
Authors :  N. Watanabe, C. Sato, I. Tanaka
Date :  18 Dec 06  (Deposition) - 18 Dec 07  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,E,G  (1x)
Biol. Unit 2:  C,D,F,H  (1x)
Biol. Unit 3:  I,J  (1x)
Keywords :  Type Ii Restriction Enzyme Hindiii(E. C. 3. 1. 21. 4)/Dna, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Watanabe, Y. Takasaki, C. Sato, S. Ando, I. Tanaka
Structures Of Restriction Endonuclease Hindiii In Complex With Its Cognate Dna And Divalent Cations
Acta Crystallogr. , Sect. D V. 65 1326 2009
PubMed-ID: 19966419  |  Reference-DOI: 10.1107/S0907444909041134

(-) Compounds

Molecule 1 - TYPE II RESTRICTION ENZYME HINDIII
    Chains: A, C, B, D
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HINDIIIR
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 71421
    Strain: RD KW20
    Synonym: ENDONUCLEASE HINDIII, R.HINDIII
 
Molecule 2 - DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)- 3')
    Chains: E, F, G, H, I, J
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): AB  E G   
Biological Unit 2 (1x):   CD F H  
Biological Unit 3 (1x):         IJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN C:209 , ASP C:214 , HOH C:2016BINDING SITE FOR RESIDUE ACT C 2001
2AC2SOFTWAREASP B:161 , SER B:199 , THR B:202 , ALA B:207BINDING SITE FOR RESIDUE ACT B 2002
3AC3SOFTWAREPHE C:186 , LEU C:222 , PHE C:223 , LYS C:224 , HOH C:2145BINDING SITE FOR RESIDUE ACT C 2003
4AC4SOFTWAREGLY A:89 , LYS B:152 , DC E:2 , DC E:3 , HOH E:1007 , HOH E:1010 , DG G:11BINDING SITE FOR RESIDUE GOL E 1001
5AC5SOFTWAREARG C:296 , TYR C:298 , PHE D:145 , PHE D:146 , TYR D:148 , PRO D:149 , ASN D:210 , MET D:212BINDING SITE FOR RESIDUE GOL C 1002
6AC6SOFTWAREPHE C:145 , PHE C:146 , TYR C:148 , PRO C:149 , ASN C:210 , MET C:212 , ARG D:296 , TYR D:298BINDING SITE FOR RESIDUE GOL C 1003
7AC7SOFTWAREPHE A:145 , PHE A:146 , TYR A:148 , PRO A:149 , ASN A:210 , MET A:212 , ARG B:296 , TYR B:298BINDING SITE FOR RESIDUE GOL A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E52)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn C:261 -Phe C:262
2Thr D:263 -Arg D:264
3Arg D:264 -Glu D:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E52)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E52)

(-) Exons   (0, 0)

(no "Exon" information available for 2E52)

(-) 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:299
 aligned with T2D3_HAEIN | P43870 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:299
                                    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       261       271       281       291         
           T2D3_HAEIN     2 KKSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 300
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhh.ee........hhhhhhhhhhhhhhhhhhhh..eeeee.........eeeee.....eeeeee..ee.......hhhh.hhhhhhh.....eeeeee.hhhh.....hhhhhhhhh.eeeeehhhhhhhhh...........hhhhhhhhhhh....hhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e52 A   1 KKSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with T2D3_HAEIN | P43870 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:298
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292        
           T2D3_HAEIN     3 KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 300
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhh..ee........hhhhhhhhhhhhhhhhhhhh..eeeee.........eeeee.....eeeeee..ee.......hhhh.hhhhhhh.....eeeeee.hhh......hhhhhhhhh..eeeehhhhhhhhh...........hhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e52 B   2 KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 299
                                    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       261       271       281       291        


Chain C from PDB  Type:PROTEIN  Length:299
 aligned with T2D3_HAEIN | P43870 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:299
                                    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       261       271       281       291         
           T2D3_HAEIN     2 KKSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 300
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhh.ee........hhhhhhhhhhhhhhhhhhhh..eeeee.........eeeee.....eeeeee..ee.......hhhh.hhhhhhh.....eeeeee.hhh......hhhhhhhhh.eeeeehhhhhhhhh...........hhhhhhhhhhh....hhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e52 C   1 KKSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain D from PDB  Type:PROTEIN  Length:298
 aligned with T2D3_HAEIN | P43870 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:298
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292        
           T2D3_HAEIN     3 KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 300
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh..ee........hhhhhhhhhhhhhhhhhhhh..eeeee.........eeeee.....eeeeee..ee.......hhhh.hhhhhhh.....eeeeee.hhh......hhhhhhhhh..eeeehhhhhhhhh...........hhhhhhhhhhh....hhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhh..hhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e52 D   2 KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 299
                                    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       261       271       281       291        


Chain E from PDB  Type:DNA  Length:12
                                            
                 2e52 E   1 GCCAAGCTTGGC  12
                                    10  


Chain F from PDB  Type:DNA  Length:12
                                            
                 2e52 F   1 GCCAAGCTTGGC  12
                                    10  


Chain G from PDB  Type:DNA  Length:12
                                            
                 2e52 G   1 GCCAAGCTTGGC  12
                                    10  


Chain H from PDB  Type:DNA  Length:12
                                            
                 2e52 H   1 GCCAAGCTTGGC  12
                                    10  


Chain I from PDB  Type:DNA  Length:12
                                            
                 2e52 I   1 GCCAAGCTTGGC  12
                                    10  


Chain J from PDB  Type:DNA  Length:12
                                            
                 2e52 J   1 GCCAAGCTTGGC  12
                                    10
   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 2E52)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E52)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E52)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (T2D3_HAEIN | P43870)
molecular function
    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.
    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.
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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  2e52
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  T2D3_HAEIN | P43870
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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
        T2D3_HAEIN | P43870: 3a4k 3wvg 3wvh 3wvi 3wvk 3wvp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2E52)