1IAW | PD0207 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NAEI COMPLEXED WITH 17MER DNA

Authors :   Q. Huai, J. D. Colandene, M. D. Topal, H. Ke

Date :   23 Mar 01 (Deposition) - 03 Aug 01 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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

Reference :   Q. Huai, J. D. Colandene, M. D. Topal, H. Ke
Structure Of Naei-Dna Complex Reveals Dual-Mode Dna Recognition And Complete Dimer Rearrangement.
Nat. Struct. Biol. V. 8 665 2001
PubMed-ID: 11473254 | Reference-DOI: 10.1038/90366

*Molecule 1 - 5'-D(TPGPCPCPAPCPGPCPCPGPGPCPGPTPGPGPC)- 3'**
	Chains	:	C, D, E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - TYPE II RESTRICTION ENZYME NAEI
	Chains	:	A, B
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMALE2
	Expression System Strain	:	CAA1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NAE I
	Organism Scientific	:	LECHEVALIERIA AEROCOLONIGENES
	Organism Taxid	:	68170

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1IAW)

(no "Site" information available for 1IAW)

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

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

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

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

(no "Exon" information available for 1IAW)

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:304
 aligned with T2N1_NOCAE | P50187 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:304
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309    
           T2N1_NOCAE    10 EPDDDLERVRATLYSLDPDGDRTAGVLRDTLDQLYDGQRTGRWNFDQLHKTEKTHMGTLVEINLHREFQFGDGFETDYEIAGVQVDCKFSMSQGAWMLPPESIGHICLVIWASDQQCAWTAGLVKVIPQFLGTANRDLKRRLTPEGRAQVVKLWPDHGKLQENLLLHIPGDVRDQIFSAKSSRGNQHGQARVNELFRRVHGRLIGRAVIATVAQQDDFMKRVRGSGGARSILRPEGIIILGHQDNDPKVANDLGLPVPRKGQVVAARVVPADEGDQRQTAEIQGRRWAVAVPGDPIVEAPVVPR 313
               SCOP domains d1iawa_ A: Restriction endonuclease NaeI                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1iawA01 A:10-176  [code=3.40.600.10, no name defined]                                                                                                                  1iawA02 A:177-309 'winged helix' repressor DNA binding domain                                                                        ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....eee..eeeeeeee........hhhhh..eeeeeeee....eeeeeeee.hhhh............hhhhhhh.ee..........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhh...hhhhhhhhh.eeee....hhhhhhhhh..........eeeeeee.........ee....eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iaw A  10 EPDDDLERVRATLYSLDPDGDRTAGVLRDTLDQLYDGQRTGRWNFDQLHKTEKTHMGTLVEINLHREFQFGDGFETDYEIAGVQVDCKFSMSQGAWMLPPESIGHICLVIWASDQQCAWTAGLVKVIPQFLGTANRDLKRRLTPEGRAQVVKLWPDHGKLQENLLLHIPGDVRDQIFSAKSSRGNQHGQARVNELFRRVHGRLIGRAVIATVAQQDDFMKRVRGSGGARSILRPEGIIILGHQDNDPKVANDLGLPVPRKGQVVAARVVPADEGDQRQTAEIQGRRWAVAVPGDPIVEAPVVPR 313
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309

Chain B from PDB  Type:PROTEIN  Length:304
 aligned with T2N1_NOCAE | P50187 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:304
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309    
           T2N1_NOCAE    10 EPDDDLERVRATLYSLDPDGDRTAGVLRDTLDQLYDGQRTGRWNFDQLHKTEKTHMGTLVEINLHREFQFGDGFETDYEIAGVQVDCKFSMSQGAWMLPPESIGHICLVIWASDQQCAWTAGLVKVIPQFLGTANRDLKRRLTPEGRAQVVKLWPDHGKLQENLLLHIPGDVRDQIFSAKSSRGNQHGQARVNELFRRVHGRLIGRAVIATVAQQDDFMKRVRGSGGARSILRPEGIIILGHQDNDPKVANDLGLPVPRKGQVVAARVVPADEGDQRQTAEIQGRRWAVAVPGDPIVEAPVVPR 313
               SCOP domains d1iawb_ B: Restriction endonuclease NaeI                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1iawB01 B:10-176  [code=3.40.600.10, no name defined]                                                                                                                  1iawB02 B:177-309 'winged helix' repressor DNA binding domain                                                                        ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........eee..eeeeeeee........hhhhh..eeeeeeeehhhheeeeeeee.hhh.eeee.....eeehhhhhhh.eee.........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...eeehhhhhhhhh...hhhhh....hhhhhhhhh.eeee....hhhhhhhhh........eeeeeeeee.........ee....eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iaw B  10 EPDDDLERVRATLYSLDPDGDRTAGVLRDTLDQLYDGQRTGRWNFDQLHKTEKTHMGTLVEINLHREFQFGDGFETDYEIAGVQVDCKFSMSQGAWMLPPESIGHICLVIWASDQQCAWTAGLVKVIPQFLGTANRDLKRRLTPEGRAQVVKLWPDHGKLQENLLLHIPGDVRDQIFSAKSSRGNQHGQARVNELFRRVHGRLIGRAVIATVAQQDDFMKRVRGSGGARSILRPEGIIILGHQDNDPKVANDLGLPVPRKGQVVAARVVPADEGDQRQTAEIQGRRWAVAVPGDPIVEAPVVPR 313
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309

Chain C from PDB  Type:DNA  Length:16
                                                
                 1iaw C   2 GCCACGCCGGCGTGGC  17
                                    11

Chain D from PDB  Type:DNA  Length:17
                                                 
                 1iaw D   1 TGCCACGCCGGCGTGGC  17
                                    10

Chain E from PDB  Type:DNA  Length:17
                                                 
                 1iaw E   1 TGCCACGCCGGCGTGGC  17
                                    10

Chain F from PDB  Type:DNA  Length:17
                                                 
                 1iaw F   1 TGCCACGCCGGCGTGGC  17
                                    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(

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Folds(

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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 NaeI (2)

Protein domain: Restriction endonuclease NaeI (2)

Nocardia aerocolonigenes [TaxId: 68170] (2)

1a	d1iawa_	A:
1b	d1iawb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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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	1iawA01	A:10-176
1b	1iawB01	B:10-176

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

[unclassified] (77)

2a	1iawA02	A:177-309
2b	1iawB02	B:177-309

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (T2N1_NOCAE | P50187)

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: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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	T2N1_NOCAE \| P50187	:	1ev7

1ev7	CRYSTAL STRUCTURE OF DNA RESTRICTION ENDONUCLEASE NAEI

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