1B94 | PD0037 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   RESTRICTION ENDONUCLEASE ECORV WITH CALCIUM

Authors :   M. P. Thomas, S. E. Halford, R. L. Brady

Date :   19 Feb 99 (Deposition) - 26 Feb 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   M. P. Thomas, R. L. Brady, S. E. Halford, R. B. Sessions, G. S. Baldwin
Structural Analysis Of A Mutational Hot-Spot In The Ecorv Restriction Endonuclease: A Catalytic Role For A Main Chain Carbonyl Group.
Nucleic Acids Res. V. 27 3438 1999
PubMed-ID: 10446231 | Reference-DOI: 10.1093/NAR/27.17.3438
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(APAPAPGPAPTPAPTPCPTPT)-3')**
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - RESTRICTION ENDONUCLEASE ECORV
	Cellular Location	:	CYTOPLASM
	Chains	:	A, B
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBSKRV
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ECORVR
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		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	CA	2	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:74 , ASP B:90 , HOH B:566 , HOH B:630 , HOH B:635 , DA D:7 , HOH D:153 , HOH D:277	BINDING SITE FOR RESIDUE CA B 501
2	AC2	SOFTWARE	ASP A:74 , ASP A:90 , HOH A:521 , HOH A:649 , DA C:7 , HOH C:297	BINDING SITE FOR RESIDUE CA A 502

(no "SS Bond" information available for 1B94)

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 1B94)

(no "PROSITE Motif" information available for 1B94)

(no "Exon" information available for 1B94)

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:244
 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 d1b94a_ A: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1b94A00 A:2-245  [code=3.40.600.10, no name defined]                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....eee.....eee....hhhhhhhhhhhhhhhhhhhhhh...eee..........eeee.......eeeeeeeeeee............................hhheeeeeeeeeeee.....hhhh....hhhhhh........eeeeeehhhh...................hhhhhh.......hhhhhhhhh.....hhhhhh....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b94 A   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 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

Chain B from PDB  Type:PROTEIN  Length:244
 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 d1b94b_ B: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1b94B00 B:2-245  [code=3.40.600.10, no name defined]                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....eee.....eee....hhhhhhhhhhhhhhhhhhhhhhh..eee..........eeee.......eeeeeeeeeee............................hhheeeeeeeeeeeee............hhhhhh....eeeeeeeeeehhhh...................hhhhhh.......hhhhhhhhh.....hhhhhh....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b94 B   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 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

Chain C from PDB  Type:DNA  Length:11
                                           
                 1b94 C   1 AAAGATATCTT  11
                                    10

Chain D from PDB  Type:DNA  Length:11
                                           
                 1b94 D   1 AAAGATATCTT  11
                                    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	d1b94a_	A:
1b	d1b94b_	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	1b94A00	A:2-245
1b	1b94B00	B:2-245

(no "Pfam Domain" information available for 1B94)

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: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.
	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.
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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	1b94
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(no "Related Entries Specified in the PDB File" available for 1B94)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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