3ZDC - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV4 DNA OLIGONUCLEOTIDE, POTASSIUM AND CALCIUM

Authors :   G. R. Hemsworth, C. S. Anstey-Gilbert, C. S. Flemming, M. R. G. Hodskins J. Zhang, S. E. Sedelnikova, T. J. Stillman, J. R. Sayers, P. J. Artymiu

Date :   26 Nov 12 (Deposition) - 10 Jul 13 (Release) - 09 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.53

Chains :   Asym./Biol. Unit : A,X

Keywords :   Hydrolase, Exoix, Flap Endonuclease, Dna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. S. Anstey-Gilbert, G. R. Hemsworth, C. S. Flemming, M. R. G. Hodskinson, J. Zhang, S. E. Sedelnikova, T. J. Stillman, J. R. Sayers, P. J. Artymiuk
The Structure Of E. Coli Exoix - Implications For Dna Binding And Catalysis In Flap Endonucleases
Nucleic Acids Res. V. 41 8357 2013
PubMed-ID: 23821668 | Reference-DOI: 10.1093/NAR/GKT591

Molecule 1 - PROTEIN XNI
	Chains	:	A
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJONEX
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PCI857
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	XL1 BLUE
	Synonym	:	EXOIX

*Molecule 2 - 5OV4 DNA, 5'-D(APAPAPAPGPCPGPTPAPCPGPCP)-3'*
	Chains	:	X
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	X

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	2	Ligand/Ion	CALCIUM ION
3	K	1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:171 , ALA A:172 , PRO A:180 , VAL A:182 , ILE A:185 , CA A:1253 , DC X:10	BINDING SITE FOR RESIDUE K A1251
2	AC2	SOFTWARE	ASP A:127 , HOH A:2058 , HOH A:2094 , HOH A:2095 , HOH A:2125	BINDING SITE FOR RESIDUE CA A1252
3	AC3	SOFTWARE	ALA A:172 , ILE A:185 , K A:1251 , HOH A:2121 , HOH A:2123 , DC X:10	BINDING SITE FOR RESIDUE CA A1253
4	AC4	SOFTWARE	GLN A:35 , LEU A:36 , ARG A:141 , LYS A:146 , HOH A:2028 , HOH A:2149	BINDING SITE FOR RESIDUE ACT A1254
5	AC5	SOFTWARE	LEU A:110 , LYS A:113 , VAL A:114	BINDING SITE FOR RESIDUE ACT A1255

(no "SS Bond" information available for 3ZDC)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:23	-	Pro A:24

(no "SAP(SNP)/Variant" information available for 3ZDC)

(no "PROSITE Motif" information available for 3ZDC)

(no "Exon" information available for 3ZDC)

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:247
 aligned with XNI_ECO57 | Q8X6R9 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
            XNI_ECO57     2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDDENRSSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWSTSGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLV 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeeeee..--..hhhhhhh..........hhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhh...eeeee....ee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zdc A   2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDDE--SSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWSTSGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLV 250
                                    11        21        31        41        51|  |    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
                                                                             52 55

Chain A from PDB  Type:PROTEIN  Length:247
 aligned with XNI_ECOLI | P38506 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
            XNI_ECOLI     2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDDENRSSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWSTSGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLV 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeeeee..--..hhhhhhh..........hhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhh...eeeee....ee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zdc A   2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDDE--SSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWSTSGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLV 250
                                    11        21        31        41        51|  |    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
                                                                             52 55

Chain X from PDB  Type:DNA  Length:12
                                            
                 3zdc X   1 AAAAGCGTACGC  12
                                    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 '\|'

(no "SCOP Domain" information available for 3ZDC)

(no "CATH Domain" information available for 3ZDC)

(no "Pfam Domain" information available for 3ZDC)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (XNI_ECO57 | Q8X6R9)

molecular function
	GO:0017108	5'-flap endonuclease activity	Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0048256	flap endonuclease activity	Catalysis of the cleavage of a flap structure in DNA, but not other DNA structures; processes the ends of Okazaki fragments in lagging strand DNA synthesis.
	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.
	GO:0030955	potassium ion binding	Interacting selectively and non-covalently with potassium (K+) ions.
biological process
	GO:0033567	DNA replication, Okazaki fragment processing	The DNA metabolic process, occurring during lagging strand synthesis, by which RNA primers are removed from Okazaki fragments, the resulting gaps filled by DNA polymerization, and the ends ligated to form a continuous strand.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

Chain A (XNI_ECOLI | P38506)

molecular function
	GO:0008409	5'-3' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
	GO:0017108	5'-flap endonuclease activity	Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0048256	flap endonuclease activity	Catalysis of the cleavage of a flap structure in DNA, but not other DNA structures; processes the ends of Okazaki fragments in lagging strand DNA synthesis.
	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.
	GO:0030955	potassium ion binding	Interacting selectively and non-covalently with potassium (K+) ions.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0033567	DNA replication, Okazaki fragment processing	The DNA metabolic process, occurring during lagging strand synthesis, by which RNA primers are removed from Okazaki fragments, the resulting gaps filled by DNA polymerization, and the ends ligated to form a continuous strand.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ 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
		Ser A:23 - Pro A:24	[ 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
	3zdc
		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
	XNI_ECO57 \| Q8X6R9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	XNI_ECOLI \| P38506
		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.-.-
		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
	XNI_ECO57 \| Q8X6R9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	XNI_ECOLI \| P38506
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	XNI_ECO57 \| Q8X6R9	:	3zd8 3zd9 3zda 3zdb 3zdd 3zde
	XNI_ECOLI \| P38506	:	3zd8 3zd9 3zda 3zdb 3zdd 3zde

3zd8	POTASSIUM BOUND STRUCTURE OF E. COLI EXOIX IN P1
3zd9	POTASSIUM BOUND STRUCTURE OF E. COLI EXOIX IN P21
3zda	STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH A FRAGMENT OF THE FLAP1 DNA OLIGOCULEOTIDE, POTASSIUM AND MAGNESIUM
3zdb	STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV4 DNA OLIGONUCLEOTIDE, DI-MAGNESIUM AND POTASSIUM
3zdd	STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV6 OLIGONUCLEOTIDE AND POTASSIUM
3zde	POTASSIUM FREE STRUCTURE OF E. COLI EXOIX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 28)

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