1D2I | PD0153 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BGLII COMPLEXED WITH DNA 16-MER

Authors :   C. M. Lukacs, R. Kucera, I. Schildkraut, A. K. Aggarwal

Date :   23 Sep 99 (Deposition) - 21 Feb 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Restriction Endonuclease, Restriction Enzyme, Protein-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Lukacs, R. Kucera, I. Schildkraut, A. K. Aggarwal
Understanding The Immutability Of Restriction Enzymes: Crystal Structure Of Bglii And Its Dna Substrate At 1. 5 A Resolution.
Nat. Struct. Biol. V. 7 134 2000
PubMed-ID: 10655616 | Reference-DOI: 10.1038/72405

*Molecule 1 - DNA (5'-D(TPAPTPTPAPTPAPGPAPTPCPTPAPTPAPA)- 3')*
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	OLIGOMERS WERE PRODUCED COMMERCIALLY
	Synthetic	:	YES

Molecule 2 - PROTEIN (RESTRICTION ENDONUCLEASE BGLII)
	Chains	:	A, B
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:84 , VAL A:94 , HOH A:625 , HOH A:657 , HOH A:729 , DG C:8	BINDING SITE FOR RESIDUE MG A 601
2	AC2	SOFTWARE	ASP B:84 , VAL B:94 , HOH B:653 , HOH B:762 , DG D:24 , HOH D:472	BINDING SITE FOR RESIDUE MG B 602

(no "SS Bond" information available for 1D2I)

(no "Cis Peptide Bond" information available for 1D2I)

(no "SAP(SNP)/Variant" information available for 1D2I)

(no "PROSITE Motif" information available for 1D2I)

(no "Exon" information available for 1D2I)

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:223
 aligned with T2B2_BACIU | Q45488 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
           T2B2_BACIU     1 MKIDITDYNHADEILNPQLWKEIEETLLKMPLHVKASDQASKVGSLIFDPVGTNQYIKDELVPKHWKNNIPIPKRFDFLGTDIDFGKRDTLVEVQFSNYPFLLNNTVRSELFHKSNMDIDEEGMKVAIIITKGHMFPASNSSLYYEQAQNQLNSLAEYNVFDVPIRLVGLIEDFETDIDIVSTTYADKRYSRTITKRDTVKGKVIDTNTPNTRRRKRGTIVTY 223
               SCOP domains d1d2ia_ A: Restriction endonuclease BglII                                                                                                                                                                                       SCOP domains
               CATH domains -1d2iA00 A:2-223  [code=3.40.91.20, no name defined]                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh---.........eeehhhhhhhhhhhhhh....eeeee.hhhhhhhh.eeeeee..eeeee....hhhhhhhhhhhhhhhhh..........eeeeeee...........hhhhhhhhhhhhhhh......eeeeeee......eeeeeeee........eeeeeeeeeeee.............eeee. Sec.struct. author (1)
     Sec.struct. author (2) -------------------------------eeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d2i A   1 mKIDITDYNHADEILNPQLWKEIEETLLKmPLHVKASDQASKVGSLIFDPVGTNQYIKDELVPKHWKNNIPIPKRFDFLGTDIDFGKRDTLVEVQFSNYPFLLNNTVRSELFHKSNmDIDEEGmKVAIIITKGHmFPASNSSLYYEQAQNQLNSLAEYNVFDVPIRLVGLIEDFETDIDIVSTTYADKRYSRTITKRDTVKGKVIDTNTPNTRRRKRGTIVTY 223
                            |       10        20        30        40        50        60        70        80        90       100       110      |120   |   130    |  140       150       160       170       180       190       200       210       220   
                            |                           30-MSE                                                                                117-MSE  |        135-MSE                                                                                    
                            1-MSE                                                                                                                    124-MSE

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with T2B2_BACIU | Q45488 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
           T2B2_BACIU     1 MKIDITDYNHADEILNPQLWKEIEETLLKMPLHVKASDQASKVGSLIFDPVGTNQYIKDELVPKHWKNNIPIPKRFDFLGTDIDFGKRDTLVEVQFSNYPFLLNNTVRSELFHKSNMDIDEEGMKVAIIITKGHMFPASNSSLYYEQAQNQLNSLAEYNVFDVPIRLVGLIEDFETDIDIVSTTYADKRYSRTITKRDTVKGKVIDTNTPNTRRRKRGTIVTY 223
               SCOP domains d1d2ib_ B: Restriction endonuclease BglII                                                                                                                                                                                       SCOP domains
               CATH domains -1d2iB00 B:2-223  [code=3.40.91.20, no name defined]                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhh..eeehhhhhhhhhhhhhhhhh.eeeee.hhhhhhhh.eeeeee..eeeee....hhhhhhhhhhhhhhhhh..........eeeeeee...........hhhhhhhhhhhhhhh......eeeeeee......eeeeeeee........eeeeeeeeeeee....-----....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d2i B   1 mKIDITDYNHADEILNPQLWKEIEETLLKmPLHVKASDQASKVGSLIFDPVGTNQYIKDELVPKHWKNNIPIPKRFDFLGTDIDFGKRDTLVEVQFSNYPFLLNNTVRSELFHKSNmDIDEEGmKVAIIITKGHmFPASNSSLYYEQAQNQLNSLAEYNVFDVPIRLVGLIEDFETDIDIVSTTYADKRYSRTITKRDTVKGKVIDTNT-----RKRGTIVTY 223
                            |       10        20        30        40        50        60        70        80        90       100       110      |120   |   130    |  140       150       160       170       180       190       200        |-    |  220   
                            1-MSE                       30-MSE                                                                                117-MSE  |        135-MSE                                                                   209   215        
                                                                                                                                                     124-MSE

Chain C from PDB  Type:DNA  Length:16
                                                
                 1d2i C   1 TATTATAGATCTATAA  16
                                    10

Chain D from PDB  Type:DNA  Length:16
                                                
                 1d2i D  17 TATTATAGATCTATAA  32
                                    26

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 BglII (3)

Protein domain: Restriction endonuclease BglII (3)

Bacillus subtilis [TaxId: 1423] (3)

1a	d1d2ia_	A:
1b	d1d2ib_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Restriction Endonuclease (20)

Homologous Superfamily: [code=3.40.91.20, no name defined] (11)

[unclassified] (8)

1a	1d2iB00	B:2-223
1b	1d2iA00	A:2-223

(no "Pfam Domain" information available for 1D2I)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (T2B2_BACIU | Q45488)

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.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 1d2i)

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	T2B2_BACIU \| Q45488	:	1dfm 1es8

1bhm	RESTRICTION ENDONUCLEASE BAMHI COMPLEXED WITH DNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (2, 2)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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