2GIH | PD0794 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   Q138F HINCII BOUND TO COGNATE DNA GTCGAC AND CA2+

Authors :   N. C. Horton, H. K. Joshi, C. Etzkorn, L. Chatwell, J. Bitinaite

Date :   28 Mar 06 (Deposition) - 18 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

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

Reference :   H. K. Joshi, C. Etzkorn, L. Chatwell, J. Bitinaite, N. C. Horton
Alteration Of Sequence Specificity Of The Type Ii Restriction Endonuclease Hincii Through An Indirect Readout Mechanism.
J. Biol. Chem. V. 281 23852 2006
PubMed-ID: 16675462 | Reference-DOI: 10.1074/JBC.M512339200
(for further references see the PDB file header)

*Molecule 1 - 5'-D(GPCPCPGPGPTPCPGPAPCPCPGPGPC)- 3'*
	Chains	:	E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - TYPE II RESTRICTION ENZYME HINCII
	Chains	:	A, B
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCCR101HINCII.R
	Expression System Strain	:	ER2393
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HINCIIR
	Mutation	:	YES
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	ENDONUCLEASE HINCII, R.HINCII

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:114 , ASP B:127 , VAL B:128 , DG E:8	BINDING SITE FOR RESIDUE CA B 401
2	AC2	SOFTWARE	ASP A:114 , ASP A:127 , VAL A:128 , HOH F:365	BINDING SITE FOR RESIDUE CA A 402

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

(no "Cis Peptide Bond" information available for 2GIH)

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

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

(no "Exon" information available for 2GIH)

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: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 d2giha_ A: Restriction endonuclease HincII                                                                                                                                                                                                                        SCOP domains
               CATH domains 2gihA00 A:2-258  [code=3.40.600.10, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....eee............hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhh...............eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhh.ee.....eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gih A   2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAFAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 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:251
 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 d2gihb_ B: Restrictio      n endonuclease HincII                                                                                                                                                                                                                  SCOP domains
               CATH domains 2gihB00 B:2-258  [cod      e=3.40.600.10, no name defined]                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhhhh..ee..------......hhhhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhh..hhhhhhhhh.hhhhhhhh...............eeee....eeeeeeeeee........eeeehhhhhhhhhhhhhhh....eeeeeeeeeeee....eeeeeeeeee.hhhhhhhh.ee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gih B   2 SFIKPIYQDINSILIGQKVKR------SGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAFAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 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       
                                               22     29

Chain E from PDB  Type:DNA  Length:14
                                              
                 2gih E   1 GCCGGTCGACCGGC  14
                                    10

Chain F from PDB  Type:DNA  Length:14
                                              
                 2gih F   1 GCCGGTCGACCGGC  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	d2giha_	A:
1b	d2gihb_	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)

[unclassified] (40)

1a	2gihB00	B:2-258
1b	2gihA00	A:2-258

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

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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	2gih
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1tx3	WILD TYPE HINCII BOUND TO COGNATE DNA GTCGAC
2gie
2gig	Q138F HINCII BOUND TO COGNATE DNA GTCGAC
2gii
2gij

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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