1NUI - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE PRIMASE FRAGMENT OF BACTERIOPHAGE T7 PRIMASE-HELICASE PROTEIN

Authors :   M. Kato, T. Ito, G. Wagner, C. C. Richardson, T. Ellenberger

Date :   31 Jan 03 (Deposition) - 27 May 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Zinc-Biding Domain, Toprim Fold, Dna Replication, Dna-Directed Rna Polymerase, Primosome, Late Protein, Atp-Binding, Transferase, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kato, T. Ito, G. Wagner, C. C. Richardson, T. Ellenberger
Modular Architecture Of The Bacteriophage T7 Primase Couple Rna Primer Synthesis To Dna Synthesis
Mol. Cell V. 11 1349 2003
PubMed-ID: 12769857 | Reference-DOI: 10.1016/S1097-2765(03)00195-3

Molecule 1 - DNA PRIMASE/HELICASE
	Chains	:	A, B
	EC Number	:	2.7.7.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-255
	Gene	:	4
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE T7
	Organism Taxid	:	10760

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:17 , CYS A:20 , CYS A:36 , CYS A:39	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	CYS B:17 , CYS B:20 , CYS B:36 , CYS B:39	BINDING SITE FOR RESIDUE ZN B 502
3	AC3	SOFTWARE	GLU A:157 , ASP A:207	BINDING SITE FOR RESIDUE MG A 601
4	AC4	SOFTWARE	ARG A:84 , ASP A:237 , HOH A:807	BINDING SITE FOR RESIDUE MG A 602
5	AC5	SOFTWARE	GLU B:157 , ASP B:207 , ASP B:209 , HOH B:805	BINDING SITE FOR RESIDUE MG B 603
6	AC6	SOFTWARE	ASP B:237	BINDING SITE FOR RESIDUE MG B 604

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TOPRIM	PS50880	Toprim domain profile.	PRIM_BPT7	151-238	2	A:151-238 B:151-238

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TOPRIM	PS50880	Toprim domain profile.	PRIM_BPT7	151-238	1	A:151-238 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TOPRIM	PS50880	Toprim domain profile.	PRIM_BPT7	151-238	1	- B:151-238

(no "Exon" information available for 1NUI)

Asymmetric 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:242
 aligned with PRIM_BPT7 | P03692 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:246
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
            PRIM_BPT7    10 VFLYHIPCDNCGSSDGNSLFSDGHTFCYVCEKWTAGNEDTKERASKRKPSGGKPMTYNVWNFGESNGRYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLPCKDANECHLNGHDREIMEQVW 255
               SCOP domains d1nuia2 A:10-63                                       d1nuia1 A:64-255 Primase fragment of primase-helicase protein                                                                                                                                    SCOP domains
               CATH domains 1nuiA01 A:10-56                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..........eeee....eee.....ee.----hhhhhhh..............hhhhh......hhhhh.hhhhhhhhheeeeee..eeeeeeeee.....eeeeeee......eeee........hhhhh......eee.hhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh....eee......hhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------TOPRIM  PDB: A:151-238 UniProt: 151-238                                                 ----------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nui A  10 VFLYHIPCDNCGSSDGNSLFSDGHTFCYVCEKWTA----TKERASKRKPSGGKPGTYNVWNFGESNGRYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLPCKDANECHLNGHDREIMEQVW 255
                                    19        29        39    |   49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
                                                             44   49

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with PRIM_BPT7 | P03692 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:246
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
            PRIM_BPT7    10 VFLYHIPCDNCGSSDGNSLFSDGHTFCYVCEKWTAGNEDTKERASKRKPSGGKPMTYNVWNFGESNGRYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLPCKDANECHLNGHDREIMEQVW 255
               SCOP domains d1nuib2 B:10-63                                       d1nuib1 B:64-255 Primase fragment of primase-helicase protein                                                                                                                                    SCOP domains
               CATH domains 1nuiB01 B:10-56                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Prim_Zn_Ribbon-1nuiB01 B:12-42 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --Prim_Zn_Ribbon-1nuiB02 B:12-42 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eee............eeee....eee......-------hhhhhh...............hhhhh.....hhhhh.hhhhhhhhheeeee....eeeeeeee.....eeeeeee.......eee......eehhhhh..eeeeeee.hhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhh....eee......hhhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------TOPRIM  PDB: B:151-238 UniProt: 151-238                                                 ----------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nui B  10 VFLYHIPCDNCGSSDGNSLFSDGHTFCYVCEKW-------KERASKRKPSGGKPGTYNVWNFGESNGRYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLPCKDANECHLNGHDREIMEQVW 255
                                    19        29        39  |      -|       59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
                                                           42      50

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Single Sheet (341)

Topology: N-terminal domain of TfIIb (166)

Homologous Superfamily: [code=2.20.25.10, no name defined] (79)

Enterobacteria phage t7. Organism_taxid: 10760. (1)

1a	1nuiA01	A:10-56
1b	1nuiB01	B:10-56

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Zn_Beta_Ribbon (109)

Family: Prim_Zn_Ribbon (1)

Enterobacteria phage T7 (Bacteriophage T7) (1)

1a	Prim_Zn_Ribbon-1nuiB01	B:12-42
1b	Prim_Zn_Ribbon-1nuiB02	B:12-42

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRIM_BPT7 | P03692)

molecular function
	GO:0043139	5'-3' DNA helicase activity	Catalysis of the unwinding of the DNA helix in the direction 5' to 3'.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003678	DNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
	GO:0003896	DNA primase activity	Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases.
	GO:0003899	DNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0032508	DNA duplex unwinding	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006269	DNA replication, synthesis of RNA primer	The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.

Asymmetric 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
		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 ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nui)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 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
	1nui
		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
	PRIM_BPT7 \| P03692
		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)
	2.7.7.-
		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
	PRIM_BPT7 \| P03692
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PRIM_BPT7 \| P03692	:	1cr0 1cr1 1cr2 1cr4 1e0j 1e0k 1q57 5ikn

(no "Related Entries Specified in the PDB File" available for 1NUI)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (16, 16)

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