1F0O | PD0149 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7.5 WITH TWO CALCIUM IONS AT EACH ACTIVE SITE

Authors :   J. R. Horton, X. Cheng

Date :   16 May 00 (Deposition) - 06 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Protein-Dna Complex, Endonuclease Type Ii, Restriction Enzyme, Catalytic Metal Visualization, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Horton, X. Cheng
Pvuii Endonuclease Contains Two Calcium Ions In Active Sites.
J. Mol. Biol. V. 300 1049 2000
PubMed-ID: 10903853 | Reference-DOI: 10.1006/JMBI.2000.3938
(for further references see the PDB file header)

*Molecule 1 - (5'-D(TPGPAPCPCPAPGPCPTPGPGPTPC-3')**
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	SELF-ANNEALING OLIGONUCLEOTIDE CONTAINING COGNATE SIX BASE PAIR SEQUENCE
	Synthetic	:	YES

Molecule 2 - TYPE II RESTRICTION ENZYME PVUII
	Chains	:	A, B
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPR594
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PROTEUS VULGARIS
	Organism Taxid	:	585
	Synonym	:	PVUII ENDONUCLEASE, R.PVUII

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:58 , GLU A:68 , LEU A:69 , LYS A:70 , HOH A:847 , DC D:9	BINDING SITE FOR RESIDUE CA A 701
2	AC2	SOFTWARE	GLU B:55 , GLY B:56 , ASP B:58 , GLU B:68 , CA B:761 , DC C:9 , HOH C:1028	BINDING SITE FOR RESIDUE CA B 725
3	AC3	SOFTWARE	ASP B:58 , GLU B:68 , LEU B:69 , CA B:725 , HOH B:762 , DC C:9 , HOH C:898	BINDING SITE FOR RESIDUE CA B 761
4	AC4	SOFTWARE	GLY A:56 , ASP A:58 , GLU A:68 , DG D:8 , DC D:9 , HOH D:981	BINDING SITE FOR RESIDUE CA A 784

(no "SS Bond" information available for 1F0O)

(no "Cis Peptide Bond" information available for 1F0O)

(no "SAP(SNP)/Variant" information available for 1F0O)

(no "PROSITE Motif" information available for 1F0O)

(no "Exon" information available for 1F0O)

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
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Chain A from PDB  Type:PROTEIN  Length:154
 aligned with T2P2_PROHU | P23657 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           T2P2_PROHU     2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
               SCOP domains d1f0oa_ A: Restriction endonuclease PvuII                                                                                                                    SCOP domains
               CATH domains 1f0oA00 A:2-157 PVUII Endonuclease, subunit A                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.ee..--....ee.....eeeeeeee.....ee......hhhhhhhhhh..eeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhh.........eehhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f0o A   2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLP--EGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
                                    11        21        31        41        51|  |    61        71        81        91       101       111       121       131       141       151      
                                                                             52 55

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with T2P2_PROHU | P23657 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153    
           T2P2_PROHU     4 PDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
               SCOP domains d1f0ob_ B: Restriction endonuclease PvuII                                                                                                                  SCOP domains
               CATH domains 1f0oB00 B:4-157 PVUII Endonuclease, subunit A                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.ee..--....ee.....eeeeeeee.....ee......hhhhhhhhh...eeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhh.........eehhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f0o B   4 PDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLP--EGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
                                    13        23        33        43        |- |      63        73        83        93       103       113       123       133       143       153    
                                                                           52 55

Chain C from PDB  Type:DNA  Length:13
                                             
                 1f0o C   2 TGACCAGCTGGTC  14
                                    11

Chain D from PDB  Type:DNA  Length:13
                                             
                 1f0o D   2 TGACCAGCTGGTC  14
                                    11

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: Restriction endonuclease PvuII (10)

Protein domain: Restriction endonuclease PvuII (9)

Proteus vulgaris [TaxId: 585] (9)

1a	d1f0oa_	A:
1b	d1f0ob_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: PvuII Endonuclease; Chain A (9)

Homologous Superfamily: PVUII Endonuclease, subunit A (9)

[unclassified] (5)

1a	1f0oA00	A:2-157
1b	1f0oB00	B:4-157

(no "Pfam Domain" information available for 1F0O)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (T2P2_PROHU | P23657)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1f0o)

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	1f0o
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	3.1.21.4
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UniProtKB/Swiss-Prot
	T2P2_PROHU \| P23657	:	1eyu 1h56 1k0z 1ni0 1pvi 1pvu 2pvi 3ksk 3pvi

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

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)

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Gene Ontology (7, 7)

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