2OXV - JenaLib

Title :   STRUCTURE OF THE A138T PROMISCUOUS MUTANT OF THE ECORI RESTRICTION ENDONUCLEASE BOUND TO ITS COGNATE RECOGNITION SITE.

Authors :   P. J. Sapienza, J. M. Rosenberg, L. Jen-Jacobson

Date :   21 Feb 07 (Deposition) - 23 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Ecori, Type Ii Restriction Endonuclease, Protein-Dna Interactions, Promiscuous Mutant, Relaxed Specificity Mutant, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. J. Sapienza, J. M. Rosenberg, L. Jen-Jacobson
Structural And Thermodynamic Basis For Enhanced Dna Binding By A Promiscuous Mutant Ecori Endonuclease.
Structure V. 15 1368 2007
PubMed-ID: 17997963 | Reference-DOI: 10.1016/J.STR.2007.09.014
(for further references see the PDB file header)

Compounds

Molecule 1 - TYPE II RESTRICTION ENZYME ECORI
	Chains	:	A
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ECORIR
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ENDONUCLEASE ECORI, R.ECORI

*Molecule 2 - DNA (5'- D(TPCPGPCPGPAPAPTPTPCPGPCPG)-3')**
	Chains	:	C
	Engineered	:	YES
	Other Details	:	ABI3900 DNA SYNTHESIZER
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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

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)
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Chain A from PDB  Type:PROTEIN  Length:261
 aligned with T2E1_ECOLX | P00642 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:261
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276 
           T2E1_ECOLX    17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMAAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 277
               SCOP domains d2oxva_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2oxvA00 A:17-277 Eco RI Endonuclease, subunit A                                                                                                                                                                                                                       CATH domains
               Pfam domains EcoRI-2oxvA01 A:17-273                                                                                                                                                                                                                                           ---- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....eeee..eehhhhhhhhhhhh............ee.....eeeee.....eeeeeeeeeee..hhhhhhhh................hhhhhhhhhhhhhhhhh.......eeeeee........eeee.....eeee........hhhhhhhhhh...........eee......eee...eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oxv A  17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMTAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 277
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276

Chain C from PDB  Type:DNA  Length:13
                                             
                 2oxv C   1 TCGCGAATTCGCG  13
                                    10

Legend:		→ Mismatch	(orange background)
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		→ 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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (T2E1_ECOLX | P00642)

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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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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