2QNF - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF T4 ENDONUCLEASE VII H43N MUTANT IN COMPLEX WITH HETERODUPLEX DNA CONTAINING BASE MISMATCHES

Authors :   C. Biertumpfel, W. Yang, D. Suck

Date :   18 Jul 07 (Deposition) - 29 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   T4 Endonuclease Vii, Endo Vii, Resolvase, Resolving-Enzyme, Dna Mismatch, Alternative Initiation, Calcium, Hydrolase, Metal-Binding, Zinc, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Biertumpfel, W. Yang, D. Suck
Crystal Structure Of T4 Endonuclease Vii Resolving A Holliday Junction.
Nature V. 449 616 2007
PubMed-ID: 17873859 | Reference-DOI: 10.1038/NATURE06152
(for further references see the PDB file header)

Molecule 1 - RECOMBINATION ENDONUCLEASE VII
	Chains	:	A, B
	EC Number	:	3.1.22.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24D
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	49
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665
	Synonym	:	ENDO VII, PROTEIN GP49

*Molecule 2 - DNA (5'- D(DCPDAPDCPDAPDTPDCPDGPDAPDTPDGPDGPDAPDGPDCP DCPDG)-3')*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'- D(DGPDCPDGPDCPDTPDCPDCPDAPDTPDCPDGPDAPDTPDGP DTPDG)-3')*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 4 - DNA (5'- D(DCPDGPDGPDCPDTPDCPDCPDAPDTPDCPDGPDAPDTPDGP DTPDG)-3')*
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 5 - DNA (5'- D(DCPDAPDCPDAPDTPDCPDGPDAPDTPDGPDGPDAPDGPDCP DGPDC)-3')*
	Chains	:	F
	Engineered	:	YES
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:23 , CYS A:26 , CYS A:58 , CYS A:61	BINDING SITE FOR RESIDUE ZN A 158
2	AC2	SOFTWARE	CYS B:23 , CYS B:26 , CYS B:58 , CYS B:61	BINDING SITE FOR RESIDUE ZN B 158

(no "SS Bond" information available for 2QNF)

(no "Cis Peptide Bond" information available for 2QNF)

(no "SAP(SNP)/Variant" information available for 2QNF)

(no "PROSITE Motif" information available for 2QNF)

(no "Exon" information available for 2QNF)

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:157
 aligned with END7_BPT4 | P13340 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
            END7_BPT4     1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDHELNGPKAGKVRGLLCNLCNAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 157
               SCOP domains d2qnfa2 A:1-103 Recombination endonuclease VII, N-terminal domain                                      d2qnfa1 A:104-157                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------2qnfA02 A:103-153                                  ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.............hhhhheeee...........eeeeehhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.........hhhhhhhhhhhhh.hhhhhhhhhhh.........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qnf A   1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDNELNGPKAGKVRGLLCNLCNAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with END7_BPT4 | P13340 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
            END7_BPT4     1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDHELNGPKAGKVRGLLCNLCNAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 157
               SCOP domains d2qnfb2 B:1-103 Recombination endonuclease VII, N-terminal domain                                      d2qnfb1 B:104-157                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------2qnfB02 B:103-153                                  ---- CATH domains
           Pfam domains (1) Endonuclease_7-2qnfB03 B:1-97                                                                    ------Endonuc-dimeris-2qnfB01 B:104-157                      Pfam domains (1)
           Pfam domains (2) Endonuclease_7-2qnfB04 B:1-97                                                                    ------Endonuc-dimeris-2qnfB02 B:104-157                      Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhh.............hhhhheeee...........eeeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhhhhhhh........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qnf B   1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDNELNGPKAGKVRGLLCNLCNAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:DNA  Length:16
                                                
                 2qnf C   1 CACATCGATGGAGCCG  16
                                    10

Chain D from PDB  Type:DNA  Length:16
                                                
                 2qnf D   1 GCGCTCCATCGATGTG  16
                                    10

Chain E from PDB  Type:DNA  Length:16
                                                
                 2qnf E   1 CGGCTCCATCGATGTG  16
                                    10

Chain F from PDB  Type:DNA  Length:16
                                                
                 2qnf F   1 CACATCGATGGAGCGC  16
                                    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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 (23)

Homologous Superfamily: [code=1.10.720.10, no name defined] (10)

Enterobacteria phage t4. Organism_taxid: 10665. (3)

1a	2qnfA02	A:103-153
1b	2qnfB02	B:103-153

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HeH (20)

Family: Endonuc-dimeris (2)

Enterobacteria phage T4 (Bacteriophage T4) (2)

1a	Endonuc-dimeris-2qnfB01	B:104-157
1b	Endonuc-dimeris-2qnfB02	B:104-157

Clan: His-Me_finger (38)

Family: Endonuclease_7 (2)

Enterobacteria phage T4 (Bacteriophage T4) (2)

2a	Endonuclease_7-2qnfB03	B:1-97
2b	Endonuclease_7-2qnfB04	B:1-97

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (END7_BPT4 | P13340)

molecular function
	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: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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		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qnf)

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	2qnf
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	3.1.22.4
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UniProtKB/Swiss-Prot
	END7_BPT4 \| P13340	:	1e7d 1e7l 1en7 2qnc

1e7d	ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4
1e7l	ENDONUCLEASE VII (ENDOVII) N62D MUTANT FROM PHAGE T4
1en7	ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4
2qnc	T4 ENDONUCLEASE VII N62D MUTANT IN COMPLEX WITH A DNA HOLLIDAY JUNCTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 4)

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