1SUZ | PD0530 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE STRUCTURE OF K92A ECORV BOUND TO COGNATE DNA AND MG2+

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

Date :   26 Mar 04 (Deposition) - 06 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Protein-Dna Complex, Phosphoryltransfer, Hydrolase/Dna Complex (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
	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 Strain	:	MM294
	Expression System Taxid	:	562
	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 (2, 4)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:74 , ASP B:90 , HOH B:413 , HOH B:414 , DT D:6 , DA D:7 , HOH D:31	BINDING SITE FOR RESIDUE MG B 401
2	AC2	SOFTWARE	ASP A:74 , ASP A:90 , HOH A:425 , HOH A:428 , DT C:6 , DA C:7 , HOH C:49	BINDING SITE FOR RESIDUE MG A 402
3	AC3	SOFTWARE	THR A:106 , HOH A:540 , DA C:7 , DT C:8 , HOH C:195	BINDING SITE FOR RESIDUE NA A 403
4	AC4	SOFTWARE	THR B:106 , HOH B:427 , HOH B:497 , DA D:7 , DT D:8	BINDING SITE FOR RESIDUE NA B 404

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

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 1SUZ)

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

(no "Exon" information available for 1SUZ)

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:243
 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 d1suza_ A: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1suzA00 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..hhhhhhhh.......eeeeeehhhhh..........eee....hhhhhhhh.....hhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1suz A   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIATTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVAT-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    
                                                                                                                                                                       143 |                                                                                                    
                                                                                                                                                                         145

Chain B from PDB  Type:PROTEIN  Length:237
 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 d1suzb_ B: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1suzB00 B:2-245  [code=3.40.600.10, no name defined]                                                                                                                                                                                                 CATH domains
           Pfam domains (1) ---Endonuc-EcoRV-1suzB01 B:5-244                                                                                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) ---Endonuc-EcoRV-1suzB02 B:5-244                                                                                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeee....eee...hhhhhhhhhhhhhhhhhhhhhhhh..eee..........eeee.......eeeeeeeeeee.---.....eeee..............hhh.eeeeeeeeeeee...----.....hhhhhhhh.......eeeeeehhhhh..........eee....hhhhhhhh.....hhhhhhhhhhh...hhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1suz B   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIATTYTN---EKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVA----SLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 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    
                                                                                                                          97 101                                      142  147

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

Chain D from PDB  Type:DNA  Length:10
                                          
                 1suz 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	d1suza_	A:
1b	d1suzb_	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	1suzB00	B:2-245
1b	1suzA00	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-1suzB01	B:5-244
1b	Endonuc-EcoRV-1suzB02	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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:72 - Pro A:73	[ RasMol ]
		Tyr B:72 - Pro B:73	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1suz
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	T2E5_ECOLX \| P04390
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.21.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	T2E5_ECOLX \| P04390
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1SUZ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File