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Title :   STRUCTURE OF THE Y94F MUTANT OF THE RESTRICTION ENDONUCLEASE PVUII

Authors :   P. A. Tucker, M. Kokkinidis, S. Nicolaki, D. Kotsifaki

Date :   20 Dec 02 (Deposition) - 04 Feb 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (2x)
Biol. Unit 2: B,C  (1x)

Keywords :   Restriction Endonuclease, Pvuii, Point Mutation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. A. Tucker, M. Kokkinidis, S. Nicolaki, D. Kotsifaki
Structure Of The Y94F Mutant Of The Restriction Endonuclease Pvuii
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TYPE II RESTRICTION ENZYME PVUII
	Chains	:	A, B, C
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	N-A
	Expression System Strain	:	N/A
	Expression System Taxid	:	562
	Expression System Vector Type	:	N/A
	Gene	:	PVUIIR
	Mutation	:	YES
	Organism Scientific	:	PROTEUS VULGARIS
	Organism Taxid	:	585
	Synonym	:	ENDONUCLEASE PVUII, R.PVUII

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1NI0)

(no "Site" information available for 1NI0)

(no "SS Bond" information available for 1NI0)

(no "Cis Peptide Bond" information available for 1NI0)

(no "SAP(SNP)/Variant" information available for 1NI0)

(no "PROSITE Motif" information available for 1NI0)

(no "Exon" information available for 1NI0)

Asymmetric 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:157
 aligned with T2P2_PROHU | P23657 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:157
                                                                                                                                                                                    157  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152    |  
           T2P2_PROHU     3 HPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY--   -
               SCOP domains d1ni0a_ A: Restriction endonuclease PvuII                                                                                                                     SCOP domains
               CATH domains 1ni0A00 A:3-159 PVUII Endonuclease, subunit A                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.ee........ee.....eeeeeeee.....ee......hhhhhhhhh...eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhh..........eehhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ni0 A   3 HPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKFRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIYAA 159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

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

    Alignment length:157
                                                                                                                                                                                    157  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152    |  
           T2P2_PROHU     3 HPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY--   -
               SCOP domains d1ni0b_ B: Restriction endonuclease PvuII                                                                                                                     SCOP domains
               CATH domains 1ni0B00 B:3-159 PVUII Endonuclease, subunit A                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.ee........ee.....eeeeeeee.....ee....eehhhhhhhhhh..eeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhh....ee...eehhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ni0 B   3 HPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKFRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIYAA 159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain C from PDB  Type:PROTEIN  Length:158
 aligned with T2P2_PROHU | P23657 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:158
                                                                                                                                                                                     157  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     |  
           T2P2_PROHU     2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY--   -
               SCOP domains d1ni0c_ C: Restriction endonuclease PvuII                                                                                                                      SCOP domains
               CATH domains 1ni0C00 C:2-159 PVUII Endonuclease, subunit A                                                                                                                  CATH domains
           Pfam domains (1) -Endonuc-PvuII-1ni0C01 C:3-157                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) -Endonuc-PvuII-1ni0C02 C:3-157                                                                                                                              -- Pfam domains (2)
           Pfam domains (3) -Endonuc-PvuII-1ni0C03 C:3-157                                                                                                                              -- Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.ee.......eee.....eeeeeeee......ee.....hhhhhhhhh...eeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh.........eehhhhhhhhheeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ni0 C   2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKFRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIYAA 159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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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	d1ni0a_	A:
1b	d1ni0b_	B:
1c	d1ni0c_	C:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: PvuII Endonuclease; Chain A (9)

Homologous Superfamily: PVUII Endonuclease, subunit A (9)

Proteus vulgaris. Organism_taxid: 585. (2)

1a	1ni0A00	A:3-159
1b	1ni0B00	B:3-159
1c	1ni0C00	C:2-159

Asymmetric Unit

Clans(

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Families(

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Organisms( (-)

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

Family: Endonuc-PvuII (7)

Proteus hauseri (7)

1a	Endonuc-PvuII-1ni0C01	C:3-157
1b	Endonuc-PvuII-1ni0C02	C:3-157
1c	Endonuc-PvuII-1ni0C03	C:3-157

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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.

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

1pvu	NATIVE STRUCTURE OF PVUII
3pvi	STRUCTURE OF PVUII IN COMPLEX WITH DNA

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