1SX8 | PD0532 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   ECORV BOUND TO COGNATE DNA AND MN2+

Authors :   N. C. Horton, J. J. Perona

Date :   30 Mar 04 (Deposition) - 06 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

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

Reference :   N. C. Horton, J. J. Perona
Dna Cleavage By Ecorv Endonuclease: Two Metal Ions In Three Metal Ion Binding Sites
Biochemistry V. 43 6841 2004
PubMed-ID: 15170321 | Reference-DOI: 10.1021/BI0499056
(for further references see the PDB file header)

*Molecule 1 - 5'-D(CAPAPGPAPTPAPTPCPTPT)-3'**
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	SYNTHETIC
	Synthetic	:	YES

Molecule 2 - TYPE II RESTRICTION ENZYME ECORV
	Chains	:	A, B
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBSRV
	Expression System Strain	:	MM294 (ENDI-, PRO-, THI-, RK- MK+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ECORVR
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ENDONUCLEASE ECORV, R.ECORV

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	MN	6	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:74 , ASP A:90 , HOH A:258 , DT C:6 , DA C:7	BINDING SITE FOR RESIDUE MN A 246
2	AC2	SOFTWARE	GLU A:45 , ASP A:74 , HOH A:257	BINDING SITE FOR RESIDUE MN A 247
3	AC3	SOFTWARE	HIS A:71	BINDING SITE FOR RESIDUE MN A 248
4	AC4	SOFTWARE	HIS B:71 , DT C:11	BINDING SITE FOR RESIDUE MN B 246
5	AC5	SOFTWARE	ASP B:74 , ASP B:90 , HOH B:257 , HOH B:274 , DA D:7	BINDING SITE FOR RESIDUE MN B 247
6	AC6	SOFTWARE	GLU B:45 , ASP B:74 , HOH B:258	BINDING SITE FOR RESIDUE MN B 248

(no "SS Bond" information available for 1SX8)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:72	-	Pro A:73
2	Tyr B:72	-	Pro B:73

(no "SAP(SNP)/Variant" information available for 1SX8)

(no "PROSITE Motif" information available for 1SX8)

(no "Exon" information available for 1SX8)

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:241
 aligned with T2E5_ECOLX | P04390 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
           T2E5_ECOLX     2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 245
               SCOP domains d1sx8a_ A: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1sx8A00 A:2-245  [code=3.40.600.10, no name defined]                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeee...eee....hhhhhhhhhhhhhhhhhhhhhhhh..eee..........eeee.......eeeeeeeeeee.........eeee..............hhh.eeeeeeeeeeee..---hhhhh.ee.hhhhhh.......eeeeeehhhheeeee......eeee...hhhhhhhh.....hhhhhhhhhhh...hhhhhh....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sx8 A   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIATTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRV---KSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   |   151       161       171       181       191       201       211       221       231       241    
                                                                                                                                                                     141 145

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with T2E5_ECOLX | P04390 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
           T2E5_ECOLX     2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 245
               SCOP domains d1sx8b_ B: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1sx8B00 B:2-245  [code=3.40.600.10, no name defined]                                                                                                                                                                                                 CATH domains
           Pfam domains (1) ---Endonuc-EcoRV-1sx8B01 B:5-244                                                                                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) ---Endonuc-EcoRV-1sx8B02 B:5-244                                                                                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeee...eeee...hhhhhhhhhhhhhhhhhhhhhhh...eee..........eeee.......eeeeeeeeeee.----....eeee..............hhh.eeeeeeeeeeeee.-----....ee.hhhhhh...eeeeeeeeeehhhheeeeeee....eeee...hhhhhhhh.....hhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sx8 B   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIATTYTN----KIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRV-----SLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 245
                                    11        21        31        41        51        61        71        81        91     |   -|      111       121       131       141     | 151       161       171       181       191       201       211       221       231       241    
                                                                                                                          97  102                                    141   147

Chain C from PDB  Type:DNA  Length:10
                                          
                 1sx8 C   2 AAGATATCTT  11
                                    11

Chain D from PDB  Type:DNA  Length:10
                                          
                 1sx8 D   1 CAAGATATCT  10
                                    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 EcoRV (30)

Protein domain: Restriction endonuclease EcoRV (30)

Escherichia coli [TaxId: 562] (30)

1a	d1sx8a_	A:
1b	d1sx8b_	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	1sx8B00	B:2-245
1b	1sx8A00	A:2-245

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Endonuc-EcoRV] (9)

Family: Endonuc-EcoRV (9)

Escherichia coli (9)

1a	Endonuc-EcoRV-1sx8B01	B:5-244
1b	Endonuc-EcoRV-1sx8B02	B:5-244

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (T2E5_ECOLX | P04390)

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: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
		Tyr A:72 - Pro A:73	[ RasMol ]
		Tyr B:72 - Pro B:73	[ RasMol ]

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	1sx8
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	3.1.21.4
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (0, 0)

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