3E3Y - JenaLib

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Title :   Q138F HINCII BOUND TO GTTAAC AND COCRYSTALLIZED WITH 5 MM CA2+

Authors :   N. C. Horton, A. C. Babic, E. J. Little, V. M. Manohar

Date :   08 Aug 08 (Deposition) - 26 Aug 08 (Release) - 20 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.13

Chains :   Asym./Biol. Unit : A,B,E,F

Keywords :   Protein-Dna Complex, Endonuclease, Indirect Readout, Hydrolase, Nuclease, Restriction System, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. C. Babic, E. J. Little, V. M. Manohar, J. Bitinaite, N. C. Horton
Dna Distortion And Specificity In A Sequence-Specific Endonuclease.
J. Mol. Biol. V. 383 186 2008
PubMed-ID: 18762194 | Reference-DOI: 10.1016/J.JMB.2008.08.032
(for further references see the PDB file header)

Molecule 1 - TYPE-2 RESTRICTION ENZYME HINDII
	Chains	:	A, B
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HINDIIR, HI0512
	Mutation	:	YES
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	R.HINDII, TYPE II RESTRICTION ENZYME HINDII, ENDONUCLEASE HINDII

*Molecule 2 - 5'- D(DGPDCPDCPDGPDGPDTPDTPDAPDAPDCPDCPDGPDGPDC)- 3'*
	Chains	:	E, F
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	NA	3	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:114 , ASP A:127 , VAL A:128 , HOH A:410 , DA F:8 , DA F:9 , HOH F:391	BINDING SITE FOR RESIDUE CA A 259
2	AC2	SOFTWARE	ASP A:127 , ILE A:142 , HOH A:297 , HOH A:459 , DT F:7 , DA F:8	BINDING SITE FOR RESIDUE NA A 260
3	AC3	SOFTWARE	ASP B:114 , ASP B:127 , VAL B:128 , HOH B:389 , DA E:8 , DA E:9 , HOH E:34	BINDING SITE FOR RESIDUE CA B 259
4	AC4	SOFTWARE	ASP B:127 , ILE B:142 , HOH B:302 , DT E:7 , DA E:8 , HOH E:17	BINDING SITE FOR RESIDUE NA B 260
5	AC5	SOFTWARE	ASP A:114 , HOH A:309 , HOH A:366 , HOH A:367 , DT F:7 , DA F:8	BINDING SITE FOR RESIDUE NA F 15

(no "SS Bond" information available for 3E3Y)

(no "Cis Peptide Bond" information available for 3E3Y)

(no "SAP(SNP)/Variant" information available for 3E3Y)

(no "PROSITE Motif" information available for 3E3Y)

(no "Exon" information available for 3E3Y)

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:242
 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 d3e3ya_ A: Restrictio              n endonuclease HincII                                                                                                                                                                                                          SCOP domains
               CATH domains 3e3yA00 A:2-258  [cod              e=3.40.600.10, no name defined]                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eee.--------------hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhh.........-.....eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhheee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3y A   2 SFIKPIYQDINSILIGQKVKR--------------FEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEK-NDTADILLVKDQFYELLDVKTRNISKSAFAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
                                    11        21|        -     |  41        51        61        71        81        91       101      |111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
                                               22             37                                                                    108 |                                                                                                                                                    
                                                                                                                                      110

Chain A from PDB  Type:PROTEIN  Length:242
 aligned with T2D2_HAEIN | P44413 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       
           T2D2_HAEIN     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKKPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
               SCOP domains d3e3ya_ A: Restrictio              n endonuclease HincII                                                                                                                                                                                                          SCOP domains
               CATH domains 3e3yA00 A:2-258  [cod              e=3.40.600.10, no name defined]                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eee.--------------hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhh.........-.....eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhheee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3y A   2 SFIKPIYQDINSILIGQKVKR--------------FEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEK-NDTADILLVKDQFYELLDVKTRNISKSAFAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
                                    11        21|        -     |  41        51        61        71        81        91       101      |111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
                                               22             37                                                                    108 |                                                                                                                                                    
                                                                                                                                      110

Chain B from PDB  Type:PROTEIN  Length:241
 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 d3e3yb_ B: Restricti               on endonuclease HincII                                                                                                                                                                                                        SCOP domains
               CATH domains 3e3yB00 B:2-257  [co               de=3.40.600.10, no name defined]                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..ee.---------------...hhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhh..hhhhhhhhh.hhhhhhhh...............eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhh.ee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3y B   2 SFIKPIYQDINSILIGQKVK---------------FEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAFAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11        21         -     |  41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
                                              21              37

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with T2D2_HAEIN | P44413 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      
           T2D2_HAEIN     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKKPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
               SCOP domains d3e3yb_ B: Restricti               on endonuclease HincII                                                                                                                                                                                                        SCOP domains
               CATH domains 3e3yB00 B:2-257  [co               de=3.40.600.10, no name defined]                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..ee.---------------...hhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhh..hhhhhhhhh.hhhhhhhh...............eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhh.ee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3y B   2 SFIKPIYQDINSILIGQKVK---------------FEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAFAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11        21         -     |  41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
                                              21              37

Chain E from PDB  Type:DNA  Length:14
                                              
                 3e3y E   1 GCCGGTTAACCGGC  14
                                    10

Chain F from PDB  Type:DNA  Length:14
                                              
                 3e3y F   1 GCCGGTTAACCGGC  14
                                    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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: Restriction endonuclease HincII (19)

Protein domain: Restriction endonuclease HincII (19)

Haemophilus influenzae [TaxId: 727] (19)

1a	d3e3ya_	A:
1b	d3e3yb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: ECO RV Endonuclease; Chain A (56)

Homologous Superfamily: [code=3.40.600.10, no name defined] (55)

Haemophilus influenzae. Organism_taxid: 727. (9)

1a	3e3yB00	B:2-257
1b	3e3yA00	A:2-258

(no "Pfam Domain" information available for 3E3Y)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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: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.

Chain A,B (T2D2_HAEIN | P44413)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.

Asymmetric/Biological Unit
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1tx3	WILD TYPE HINCII BOUND TO GTCGAC
2gij	Q138F HINCII BOUND TO GTTAAC AND CA2+ (FROM SOAKING CA2+ INTO PREFORMED CRYSTALS)
3e40
3e41
3e42
3e43
3e44
3e45

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Ligands, Modified Residues, Ions (2, 5)

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