3NHG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   RB69 DNA POLYMERASE (S565G/Y567A) TERNARY COMPLEX WITH DTTP OPPOSITE DG

Authors :   M. Wang, J. Wang, W. H. Konigsberg

Date :   14 Jun 10 (Deposition) - 26 Jan 11 (Release) - 02 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Rb69 Dna Polymerase, Fidelity, Mutation Frequencies, Kinetics, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Xia, M. Wang, H. R. Lee, A. Sinha, G. Blaha, T. Christian, J. Wang, W. Konigsberg
Variation In Mutation Rates Caused By Rb69Pol Fidelity Mutants Can Be Rationalized On The Basis Of Their Kinetic Behavior And Crystal Structures.
J. Mol. Biol. V. 406 558 2011
PubMed-ID: 21216248 | Reference-DOI: 10.1016/J.JMB.2010.12.033

Molecule 1 - DNA POLYMERASE
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	43, GP43
	Mutation	:	YES
	Organism Common	:	BACTERIOPHAGE RB69
	Organism Scientific	:	ENTEROBACTERIA PHAGE RB69
	Organism Taxid	:	12353
	Synonym	:	GP43

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

*Molecule 3 - DNA (5'-D(GPCPGPGPAPCPTPGPCPTPTPAP(DOC))-3')**
	Chains	:	P
	Engineered	:	YES
	Other Details	:	PRIMER DNA STRAND
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	P	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	DOC	1	Mod. Nucleotide	2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:411 , LEU A:412 , SER A:414 , LEU A:415 , TYR A:416 , ARG A:482 , LYS A:560 , ASN A:564 , THR A:622 , ASP A:623 , CA A:906 , CA A:908 , CA A:909 , HOH A:991 , HOH A:1048 , DOC P:115 , DG T:4 , DG T:5	BINDING SITE FOR RESIDUE TTP A 904
2	AC2	SOFTWARE	ASN A:505 , ASN A:507 , LYS A:531 , HOH A:933 , HOH A:1020	BINDING SITE FOR RESIDUE CA A 905
3	AC3	SOFTWARE	ASP A:411 , ASP A:623 , TTP A:904	BINDING SITE FOR RESIDUE CA A 906
4	AC4	SOFTWARE	GLU A:116 , HOH A:925 , HOH A:926 , HOH A:927	BINDING SITE FOR RESIDUE CA A 907
5	AC5	SOFTWARE	ASP A:411 , LEU A:412 , ASP A:623 , TTP A:904 , CA A:909	BINDING SITE FOR RESIDUE CA A 908
6	AC6	SOFTWARE	ASP A:411 , TTP A:904 , CA A:908 , HOH A:1048 , HOH A:1176	BINDING SITE FOR RESIDUE CA A 909
7	AC7	SOFTWARE	GLU A:660 , ASP A:684 , HOH A:921 , HOH A:1040 , HOH A:1186	BINDING SITE FOR RESIDUE CA A 910

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

Asymmetric/Biological Unit

No.	Residues
1	Ser A:44	-	Gln A:45
2	Ala A:46	-	Thr A:47
3	Phe A:901	-	Asp A:902

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL_BPR69	619-627	1	A:619-627

(no "Exon" information available for 3NHG)

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:903
 aligned with DPOL_BPR69 | Q38087 from UniProtKB/Swiss-Prot  Length:903

    Alignment length:903
                                    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       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900   
           DPOL_BPR69     1 MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF 903
               SCOP domains d3nhga1 A:1-375 Exonuclease domain of family B DNA polymerases                                                                                                                                                                                                                                                                                                                         d3nhga2 A:376-903 Family B DNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------DNA_pol_B_exo1-3nhgA02 A:28-293                                                                                                                                                                                                                                           --------------------------------------------------------------------DNA_pol_B-3nhgA01 A:362-856                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ----------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeee.....eeeeee....eeeee........eee....eeeeee..hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhh.eeeeeeee...............eeeeeeee....eeeeeee.ee..ee....hhhhhhh.........hhhhhh.eeeeee.hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee...ee.hhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee......................ee...eeeeee.hhhhhhhhhhh.....eeee....hhhhhhh..........ee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..eeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee..........eeeee..eeeeeeeee..eeeeeeeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..hhhhhee..ee....hhhhhhhhhhhhhh.............eeeeee..........eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nhg A   1 MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF 903
                                    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       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900

Chain P from PDB  Type:DNA  Length:13
                                             
                 3nhg P 103 GCGGACTGCTTAc 115
                                   112  |
                                      115-DOC

Chain T from PDB  Type:DNA  Length:18
                                                  
                 3nhg T   1 TCAGGTAAGCAGTCCGCG  18
                                    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 "CATH Domain" information available for 3NHG)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DNA_pol_B-like (44)

Family: DNA_pol_B (38)

Enterobacteria phage RB69 (Bacteriophage RB69) (20)

DNA_pol_B-3nhgA01

A:362-856

Clan: RNase_H (288)

Family: DNA_pol_B_exo1 (38)

Enterobacteria phage RB69 (Bacteriophage RB69) (20)

DNA_pol_B_exo1-3nhgA02

A:28-293

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DPOL_BPR69 | Q38087)

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: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: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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:46 - Thr A:47	[ RasMol ]
		Phe A:901 - Asp A:902	[ RasMol ]
		Ser A:44 - Gln A:45	[ RasMol ]

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	3nhg
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	DPOL_BPR69 \| Q38087
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	2.7.7.7
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1ig9	STRUCTURE OF THE REPLICATING COMPLEX OF A POL ALPHA FAMILY DNA POLYMERASE
3lzj	RB69 DNA POLYMERASE (Y567A) TERNARY COMPLEX WITH DCTP OPPOSITE 7,8-DIHYDRO-8-OXOGUANINE
3nci	RB69 DNA POLYMERASE TERNARY COMPLEX WITH DCTP OPPOSITE DG AT 1.8 ANGSTROM RESOLUTION
3ndk	RB69 DNA POLYMERASE (Y567A) TERNARY COMPLEX WITH DCTP OPPOSITE DG
3ne6	RB69 DNA POLYMERASE (S565G/Y567A) TERNARY COMPLEX WITH DCTP OPPOSITE DG
3ngi	RB69 DNA POLYMERASE (Y567A) TERNARY COMPLEX WITH DTTP OPPOSITE DG

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (14, 14)

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