1SKR | PD0522 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE AND DDATP

Authors :   Y. Li, S. Dutta, S. Doublie, H. M. Bdour, J. S. Taylor, T. Ellenberger

Date :   05 Mar 04 (Deposition) - 06 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B,P,T

Keywords :   Dna Polymerase, Uv-Lesion, Replication, Open, Close, Transferase/Electron Transport/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Li, S. Dutta, S. Doublie, H. M. Bdour, J. S. Taylor, T. Ellenberger
Nucleotide Insertion Opposite A Cis-Syn Thymine Dimer By A Replicative Dna Polymerase From Bacteriophage T7.
Nat. Struct. Mol. Biol. V. 11 784 2004
PubMed-ID: 15235589 | Reference-DOI: 10.1038/NSMB792
(for further references see the PDB file header)

*Molecule 1 - 5'- D(CPGPAPAPAPAPCPGPAPCGPGPCPCPAPGPTPGPCP* CPAP(2DA))-3'**
	Chains	:	P
	Engineered	:	YES
	Other Details	:	DNA PRIMER
	Synthetic	:	YES

*Molecule 2 - 5'- D(CPCPCPTPTPTPGPGPCPAPCPTPGPGPCPCPGPTPCP GPTPTPTPTPCPG)-3'*
	Chains	:	T
	Engineered	:	YES
	Other Details	:	DNA TEMPLATE
	Synthetic	:	YES

Molecule 3 - DNA POLYMERASE
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	5
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE T7
	Organism Taxid	:	10760
	Synonym	:	T7 DNA POLYMERASE

Molecule 4 - THIOREDOXIN 1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TRXA, TSNC, FIPA, B3781, C4701, Z5291, ECS4714, STM3915, STMD1.75, STY3639, T3381, SF3854, S3905
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TRX1, TRX

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	P	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	2DA	1	Mod. Nucleotide	2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2	DAD	1	Ligand/Ion	2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE
3	MG	3	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:475 , ALA A:476 , ASP A:654 , DAD A:4004	BINDING SITE FOR RESIDUE MG A 4001
2	AC2	SOFTWARE	ASP A:475 , ASP A:654 , DAD A:4004 , HOH A:5017 , HOH A:5442 , 2DA P:22	BINDING SITE FOR RESIDUE MG A 4002
3	AC3	SOFTWARE	ASP A:5 , HOH A:5031 , HOH A:5044 , HOH A:5432 , HOH A:5433	BINDING SITE FOR RESIDUE MG A 4003
4	AC4	SOFTWARE	ARG A:429 , ASP A:475 , ALA A:476 , SER A:477 , GLY A:478 , LEU A:479 , GLU A:480 , HIS A:506 , ARG A:518 , LYS A:522 , TYR A:526 , ASP A:654 , MG A:4001 , MG A:4002 , HOH A:5008 , HOH A:5055 , HOH A:5168 , HOH A:5251 , HOH A:5284 , 2DA P:22 , DT T:4 , DT T:5	BINDING SITE FOR RESIDUE DAD A 4004

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

Asymmetric/Biological Unit

No.	Residues
1	Phe A:434	-	Pro A:435
2	Ile B:75	-	Pro B:76

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ECOLI	25-43	1	B:24-42
2	DNA_POLYMERASE_A	PS00447	DNA polymerase family A signature.	DPOL_BPT7	518-537	1	A:518-537

(no "Exon" information available for 1SKR)

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:669
 aligned with DPOL_BPT7 | P00581 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:704
                                    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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700    
            DPOL_BPT7     1 MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH 704
               SCOP domains d1skra1 A:1-210 Exonuclease domain of T7 DNA polymerase                                                                                                                                                           d1skra2 A:211-704 T7 phage DNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1skrA01 A:1-232  [code=3.30.420.10, no name defined]                                                                                                                                                                                    1skrA02 A:233-414 Taq DNA Polymerase; Chain T, domain 4                                                                                                                               1skrA03 A:415-477,A:590-704                                    1skrA04 A:478-589 5' to 3' exonuclease, C-terminal subdomain                                                    1skrA03 A:415-477,A:590-704  [code=3.30.70.370, no name defined]                                                    CATH domains
               Pfam domains -RNase_H_2-1skrA01 A:2-186                                                                                                                                                                ---------------------------------------------------------------------------------------------------------------                  DNA_pol_A-1skrA02 A:316-703                                                                                                                                                                                                                                                                                                                                                                         - Pfam domains
         Sec.struct. author .eeeeeee.........eeeeeeee....eeeeehhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhh.....hhh.eeehhhhhhhhh...........hhhhh..------..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..............................------------------...........eeeeee.....hhhhhhhhhhh................hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh....ee..eee.........eee..hhhhh......hhhhhhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.-----------.....eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.......eeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_A    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1skr A   1 MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPG------ALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGI------------------DTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVE-----------KWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH 704
                                    10        20        30        40        50        60        70        80        90       100       110      |  -   |   130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      |  -         -     | 320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570    |    -      |590       600       610       620       630       640       650       660       670       680       690       700    
                                                                                                                                              117    124                                                                                                                                                                          297                316                                                                                                                                                                                                                                                                575         587

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:105
                                    13        23        33        43        53        63        73        83        93       103     
           THIO_ECOLI     4 KIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL 108
               SCOP domains d1skrb_ B: Thioredoxin                                                                                    SCOP domains
               CATH domains 1skrB00 B:3-107 Glutaredoxin                                                                              CATH domains
               Pfam domains Thioredoxin-1skrB01 B:3-106                                                                             - Pfam domains
         Sec.struct. author ..ee....hhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee......hhhhhh..ee.eeeeee..eeeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1skr B   3 KIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL 107
                                    12        22        32        42        52        62        72        82        92       102

Chain P from PDB  Type:DNA  Length:11
                                           
                 1skr P  12 GCCAGTGCCAx  22
                                    21|
                                     22-2DA

Chain T from PDB  Type:DNA  Length:13
                                             
                 1skr T   3 CTTTGGCACTGGC  15
                                    12

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RNase_H (288)

Family: RNase_H_2 (16)

Enterobacteria phage T7 (Bacteriophage T7) (16)

RNase_H_2-1skrA01

A:2-186

Clan: Thioredoxin (367)

Family: Thioredoxin (82)

Escherichia coli (strain K12) (25)

Thioredoxin-1skrB01

B:3-106

Clan: no clan defined [family: DNA_pol_A] (69)

Family: DNA_pol_A (69)

Enterobacteria phage T7 (Bacteriophage T7) (16)

DNA_pol_A-1skrA02

A:316-703

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DPOL_BPT7 | P00581)

molecular function
	GO:0008408	3'-5' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
	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:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	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:0006261	DNA-dependent DNA replication	A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0039693	viral DNA genome replication	The replication of a viral DNA genome.
	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.

Chain B (THIO_ECOLI | P0AA25)

molecular function
	GO:0016671	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
	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).
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0034599	cellular response to oxidative stress	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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0006662	glycerol ether metabolic process	The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ile B:75 - Pro B:76	[ RasMol ]
		Phe A:434 - Pro A:435	[ RasMol ]

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	1skr
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1sks	BINARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ TEMPLATE CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE
1skw	BINARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ TEMPLATE CONTAINING A DISORDERED CIS-SYN THYMINE DIMER ON THE TEMPLATE
1sl0	TERNARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ TEMPLATE CONTAINING A DISORDERED CIS-SYN THYMINE DIMER ON THE TEMPLATE AND AN INCOMING NUCLEOTIDE
1sl1	BINARY 5' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ TEMPLATE CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE
1sl2	TERNARY 5' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ TEMPLATE CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE AND AN INCOMING NUCLEOTIDE
1t7p	T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE, A NUCLEOSIDE TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR THIOREDOXIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (3, 3)

CATH Domains (5, 5)

Pfam Domains (3, 3)

Gene Ontology (25, 26)

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