1RPZ | PD0499 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-TGCAC-3' SSDNA

Authors :   J. H. Eastberg, J. Pelletier, B. L. Stoddard

Date :   03 Dec 03 (Deposition) - 17 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Kinase, Phosphatase, Alpha/Beta, P-Loop, Ssdna, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. H. Eastberg, J. Pelletier, B. L. Stoddard
Recognition Of Dna Substrates By T4 Bacteriophage Polynucleotide Kinase.
Nucleic Acids Res. V. 32 653 2004
PubMed-ID: 14754987 | Reference-DOI: 10.1093/NAR/GKH212
(for further references see the PDB file header)

*Molecule 1 - 5'-D(TPGPCPAPC)-3'**
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - POLYNUCLEOTIDE KINASE
	Chains	:	A
	EC Number	:	2.7.1.78
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PALL17
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PSET
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665
	Synonym	:	PNK, POLYNUCLEOTIDE 5'-HYDROXYL-KINASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CA	1	Ligand/Ion	CALCIUM ION
3	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
4	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 60)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	DMS	8	Ligand/Ion	DIMETHYL SULFOXIDE
4	MSE	48	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:165 , ASP A:167 , ASP A:278	BINDING SITE FOR RESIDUE CA A 700
2	AC2	SOFTWARE	GLU A:108 , HIS A:109 , ARG A:226 , LYS A:230	BINDING SITE FOR RESIDUE DMS A 800
3	AC3	SOFTWARE	GLU A:97 , LYS A:106 , VAL A:107 , ARG A:229	BINDING SITE FOR RESIDUE DMS A 801
4	AC4	SOFTWARE	GLY A:12 , SER A:13 , GLY A:14 , LYS A:15 , SER A:16 , THR A:17 , GLU A:45 , ARG A:126 , LYS A:129	BINDING SITE FOR RESIDUE ADP A 900

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

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

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

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

(no "Exon" information available for 1RPZ)

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:287
 aligned with KIPN_BPT4 | P06855 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
            KIPN_BPT4     1 MKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIMAHEERDEYKYTKKKEGIVTGMQFDTAKSILYGGDSVKGVIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWTELVKRNSKRGTKAVPIDVLRSMYKSMREYLGLPVYNGTPGKPKAVIFDVDGTLAKMNGRGPYDLEKCDTDVINPMVVELSKMYALMGYQIVVVSGRESGTKEDPTKYYRMTRKWVEDIAGVPLVMQCQREQGDTRKDDVVKEEIFWKHIAPHFDVKLAIDDRTQVVEMWRRIGVECWQVASGDF 301
               SCOP domains d1rpza2 A:1-152 Polynucleotide kinase, kinase domain                                                                                                    d1rpza1 A:153-301 Pol              ynucleotide kinase, phosphatase domain                                                                             SCOP domains
               CATH domains -1rpzA01 A:2-149 P-loop containing nucleotide triphosphate hydrolases                                                                                ---------1rpzA02 A:159-3              01  [code=3.40.50.1000, no name defined]                                                                           CATH domains
               Pfam domains ---AAA_33-1rpzA01 A:4-147                                                                                                                          ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhh....eeeehhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...........eeeeee........--------------..hhhhhhhhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhhhh......eeeee......hhhhhhhhhhhhhhhhhheeeeeee.hhhhhhhhhhhh...ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpz A   1 mKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSImAHEERDEYKYTKKKEGIVTGmQFDTAKSILYGGDSVKGVIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWTELVKRNSKRGTKAVPIDVLRSmYKSmREYLGLPVYNGTPGKPKAVIFDVDGTLAKm--------------VINPmVVELSKmYALmGYQIVVVSGRESGTKEDPTKYYRmTRKWVEDIAGVPLVmQCQREQGDTRKDDVVKEEIFWKHIAPHFDVKLAIDDRTQVVEmWRRIGVECWQVASGDF 301
                            |       10        20        30        40 |      50        60  |     70        80        90       100       110       120       130       140  |    150       160       170  |      -       190 |     200  |    210       220      |230       240 |     250       260       270       280    |  290       300 
                            |                                       42-MSE               63-MSE                                                                     139-MSE                           173-MSE        188   |      |   |                     227-MSE        242-MSE                                    285-MSE            
                            1-MSE                                                                                                                                       143-MSE                                          192-MSE  |   |                                                                                                  
                                                                                                                                                                                                                                199-MSE                                                                                                  
                                                                                                                                                                                                                                    203-MSE

Chain B from PDB  Type:DNA  Length:3
                                   
                 1rpz B 400 TGC 402

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: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1000, no name defined] (211)

[unclassified] (3)

1rpzA02

A:159-301

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

[unclassified] (24)

1rpzA01

A:2-149

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: AAA_33 (7)

Enterobacteria phage T4 (Bacteriophage T4) (5)

AAA_33-1rpzA01

A:4-147

Asymmetric Unit(hide GO term definitions)

Chain A (KIPN_BPT4 | P06855)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046404	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	Catalysis of the reaction: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.
	GO:0047846	deoxynucleotide 3'-phosphatase activity	Catalysis of the reaction: a deoxynucleoside 3'-phosphate + H2O = a deoxynucleoside + phosphate.
	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:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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.
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

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
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DMS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

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

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	1rpz
		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
	KIPN_BPT4 \| P06855
		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)
	2.7.1.78
		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
	KIPN_BPT4 \| P06855
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	KIPN_BPT4 \| P06855	:	1ltq 1ly1 1rc8 1rrc 2ia5 5uj0

1rc8	T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-GTCAC-3' SSDNA
1rrc	T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-GTC-3' SSDNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (4, 4)

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, 2)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (12, 12)

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