2QNC - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF T4 ENDONUCLEASE VII N62D MUTANT IN COMPLEX WITH A DNA HOLLIDAY JUNCTION

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 :   3.10

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

Keywords :   T4 Endonuclease Vii, Endo Vii, Holliday Junction, Four-Way Junction, Resolvase, Resolving-Enzyme, 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(DCPDGDAPDAPDGPDAPDAPDTPDTPDCPDCPDGPDGPDAPD TPDTPDAPDGPDGPDGPDAPDTPDCPDC)-3')*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'- D(DGPDGPDAPDTPDCPDCPDCPDTPDAPDAPDGPDCPDTPDCP DCPDAPDTPDCPDGPDAPDTPDGPDTPDG)-3')*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

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

*Molecule 5 - DNA (5'- D(DAPDGPDGPDCPDCPDTPDAPDGPDCPDGPDTPDCPDCPDGP DGPDAPDAPDTPDTPDCPDTPDTPDCPDG)-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 (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

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	ASP A:40 , ASP A:62 , GLU A:65 , HOH A:160 , DC D:12 , DT D:13	BINDING SITE FOR RESIDUE MG A 159
3	AC3	SOFTWARE	CYS B:23 , CYS B:26 , CYS B:58 , CYS B:61	BINDING SITE FOR RESIDUE ZN B 158
4	AC4	SOFTWARE	ASP B:40 , HIS B:41 , ARG B:54 , ASP B:62 , HOH B:161 , DC F:12 , DC F:13	BINDING SITE FOR RESIDUE MG F 24
5	AC5	SOFTWARE	GLY B:79	BINDING SITE FOR RESIDUE EDO B 159

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

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

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

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

(no "Exon" information available for 2QNC)

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 d2qnca2 A:1-103 Recombination endonuclease VII, N-terminal domain                                      d2qnca1 A:104-157                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------2qncA02 A:103-157  [code=1.10.720.10, no name defined]  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh............hhhhheeee...........eeeeehhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qnc A   1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDHELNGPKAGKVRGLLCNLCDAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 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 d2qncb2 B:1-103 Recombination endonuclease VII, N-terminal domain                                      d2qncb1 B:104-157                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------2qncB02 B:103-157  [code=1.10.720.10, no name defined]  CATH domains
           Pfam domains (1) Endonuclease_7-2qncB03 B:1-97                                                                    ------Endonuc-dimeris-2qncB01 B:104-157                      Pfam domains (1)
           Pfam domains (2) Endonuclease_7-2qncB04 B:1-97                                                                    ------Endonuc-dimeris-2qncB02 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
                 2qnc B   1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDHELNGPKAGKVRGLLCNLCDAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:DNA  Length:22
                                                      
                 2qnc C   3 AAGAATTCCGGATTAGGGATCC  24
                                    12        22

Chain D from PDB  Type:DNA  Length:24
                                                        
                 2qnc D   1 GGATCCCTAAGCTCCATCGATGTG  24
                                    10        20

Chain E from PDB  Type:DNA  Length:24
                                                        
                 2qnc E   1 CACATCGATGGAGCCGCTAGGCCT  24
                                    10        20

Chain F from PDB  Type:DNA  Length:23
                                                       
                 2qnc F   1 AGGCCTAGCGTCCGGAATTCTTC  23
                                    10        20

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	2qncA02	A:103-157
1b	2qncB02	B:103-157

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HeH (20)

Family: Endonuc-dimeris (2)

Enterobacteria phage T4 (Bacteriophage T4) (2)

1a	Endonuc-dimeris-2qncB01	B:104-157
1b	Endonuc-dimeris-2qncB02	B:104-157

Clan: His-Me_finger (38)

Family: Endonuclease_7 (2)

Enterobacteria phage T4 (Bacteriophage T4) (2)

2a	Endonuclease_7-2qncB03	B:1-97
2b	Endonuclease_7-2qncB04	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
	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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

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

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
	2qnc
		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
	END7_BPT4 \| P13340
		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)
	3.1.22.4
		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
	END7_BPT4 \| P13340
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

1e7d	ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4
1e7l	ENDONUCLEASE VII (ENDOVII) N62D MUTANT FROM PHAGE T4
1en7	ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4
2qnf	T4 ENDONUCLEASE VII H43N MUTANT IN COMPLEX WITH HETERODUPLEX DNA CONTAINING BASE MISMATCHES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (5, 5)

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 (2, 4)

CATH Domains (1, 2)

Pfam Domains (2, 4)

Gene Ontology (5, 5)

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