2PVI | PD0011 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA

Authors :   J. Horton, X. Cheng

Date :   01 Nov 98 (Deposition) - 20 Dec 99 (Release) - 15 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

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

Keywords :   Complex (Restriction Endonuclease/Dna), Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Horton, J. Bonventre, X. Cheng
How Is Modification Of The Dna Substrate Recognized By The Pvuii Restriction Endonuclease?
J. Biol. Chem. V. 379 451 1998
PubMed-ID: 9628337
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(TPGPAPCPCPAPGP(C38) PTPGPGPTPC)-3')**
	Chains	:	C, D
	Engineered	:	YES
	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 Strain	:	PR653
	Expression System Taxid	:	562
	Organism Scientific	:	PROTEUS VULGARIS
	Organism Taxid	:	585
	Synonym	:	ENDONUCLEASE PVUII, R.PVUII

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	C38	2	Mod. Nucleotide	5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	CAA	AUTHOR	ASP A:58 , GLU A:68 , LYS A:70	CATALYTIC RESIDUES
2	CAB	AUTHOR	ASP B:58 , GLU B:68 , LYS B:70	CATALYTIC RESIDUES

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

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

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

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

(no "Exon" information available for 2PVI)

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:156
 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 d2pvia_ A: Restriction endonuclease PvuII                                                                                                                    SCOP domains
               CATH domains 2pviA00 A:2-157 PVUII Endonuclease, subunit A                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh...........eee.....eeeeeeee.....ee.......hhhhhhhh...eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhh...........eehhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pvi A   2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGRAGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKARQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:156
 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 d2pvib_ B: Restriction endonuclease PvuII                                                                                                                    SCOP domains
               CATH domains 2pviB00 B:2-157 PVUII Endonuclease, subunit A                                                                                                                CATH domains
           Pfam domains (1) -Endonuc-PvuII-2pviB01 B:3-157                                                                                                                               Pfam domains (1)
           Pfam domains (2) -Endonuc-PvuII-2pviB02 B:3-157                                                                                                                               Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..ee.......eee.....eeeeeeee.....ee.......hhhhhh.....eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhh.........eehhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pvi B   2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGRAGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKARQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:DNA  Length:13
                                             
                 2pvi C   2 TGACCAGcTGGTC  14
                                   |11   
                                   9-C38

Chain D from PDB  Type:DNA  Length:13
                                             
                 2pvi D   2 TGACCAGcTGGTC  14
                                   |11   
                                   9-C38

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 PvuII (10)

Protein domain: Restriction endonuclease PvuII (9)

Proteus vulgaris [TaxId: 585] (9)

1a	d2pvia_	A:
1b	d2pvib_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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	2pviA00	A:2-157
1b	2pviB00	B:2-157

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Endonuc-PvuII] (7)

Family: Endonuc-PvuII (7)

Proteus hauseri (7)

1a	Endonuc-PvuII-2pviB01	B:3-157
1b	Endonuc-PvuII-2pviB02	B:3-157

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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	2pvi
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	T2P2_PROHU \| P23657	:	1eyu 1f0o 1h56 1k0z 1ni0 1pvi 1pvu 3ksk 3pvi

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

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

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Exons (0, 0)

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