2GIJ | PD0796 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

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

Authors :   N. C. Horton, H. K. Joshi

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

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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(GPCPCPGPGPTPTPAPAPCPCPGPGPC)- 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 (2, 3)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:114 , ASP A:127 , VAL A:128 , HOH A:412 , DA F:8 , DA F:9	BINDING SITE FOR RESIDUE CA A 401
2	AC2	SOFTWARE	ASP B:114 , ASP B:127 , VAL B:128 , HOH B:454 , HOH B:465 , DA E:8	BINDING SITE FOR RESIDUE CA B 402
3	AC3	SOFTWARE	ASP A:127 , LYS A:129 , ILE A:142 , HOH A:469 , DT F:7 , DA F:8 , HOH F:415	BINDING SITE FOR RESIDUE NA F 403

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

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

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

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

(no "Exon" information available for 2GIJ)

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:245
 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 d2gija_ A: Restrictio            n endonuclease HincII                                                                                                                                                                                                            SCOP domains
               CATH domains 2gijA00 A:2-258  [cod            e=3.40.600.10, no name defined]                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eee.------------.hhhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhh...............eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhhh....eeeeeeeeeeee...eeeeeeeeeee.hhhhhhhh.ee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gij A   2 SFIKPIYQDINSILIGQKVKR------------EPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAFAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 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           35

Chain B from PDB  Type:PROTEIN  Length:236
 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 d2gijb_ B: Restri                  ction endonuclease HincII                                                                                                                                                                                                     SCOP domains
               CATH domains 2gijB00 B:2-257                    [code=3.40.600.10, no name defined]                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..------------------...hhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhh...............eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeeee--....eeeeeeeee.hhhhhhhheee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gij B   2 SFIKPIYQDINSILIGQ------------------FEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAFAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWE--GEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11      |  -         -     |  41        51        61        71        81        91       101       111       121       131       141       151       161       171  |  | 181       191       201       211       221       231       241       251      
                                           18                 37                                                                                                                                      174  |                                                                                
                                                                                                                                                                                                         177

Chain E from PDB  Type:DNA  Length:14
                                              
                 2gij E   1 GCCGGTTAACCGGC  14
                                    10

Chain F from PDB  Type:DNA  Length:14
                                              
                 2gij 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	d2gija_	A:
1b	d2gijb_	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	2gijB00	B:2-257
1b	2gijA00	A:2-258

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

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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gij)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2gij
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	T2C2_HAEIF \| P17743
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.21.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	T2C2_HAEIF \| P17743
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1tx3	WILD TYPE HINCII BOUND TO COGNATE DNA GTCGAC
2gie
2gig	Q138F HINCII BOUND TO COGNATE DNA GTCGAC
2gih	Q138F HINCII BOUND TO COGNATE DNA GTCGAC AND CA2+
2gii	Q138F HINCII BOUND TO COGNATE DNA GTTAAC

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File