3F2B - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   DNA POLYMERASE POLC FROM GEOBACILLUS KAUSTOPHILUS COMPLEX WITH DNA, DGTP, MG AND ZN

Authors :   D. R. Davies, R. J. Evans, J. M. Bullard, J. Christensen, L. S. Green, J. W W. K. Ribble, N. Janjic, T. C. Jarvis

Date :   29 Oct 08 (Deposition) - 20 Jan 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

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

Keywords :   Dna Polymerase C, Dna Polymerase Iii, Ternary Complex, Protein-Dna Complex, Replicative Dna Polymerase, Dna Replication, Dna-Directed Dna Polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. J. Evans, D. R. Davies, J. M. Bullard, J. Christensen, L. S. Green, J. W. Guiles, J. D. Pata, W. K. Ribble, N. Janjic, T. C. Jarvis
Structure Of Polc Reveals Unique Dna Binding And Fidelity Determinants.
Proc. Natl. Acad. Sci. Usa V. 105 20695 2008
PubMed-ID: 19106298 | Reference-DOI: 10.1073/PNAS.0809989106

Molecule 1 - DNA-DIRECTED DNA POLYMERASE III ALPHA CHAIN
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	GKAPOLC, DELTA 1-227, DELTA 412-617
	Gene	:	GK1258, POLC
	Organism Scientific	:	GEOBACILLUS KAUSTOPHILUS
	Organism Taxid	:	1462

*Molecule 2 - 5'-D(DCPDAPDGPDTPDGPDAPDGPDAPDCPDGPDGPDGPDCPD APDAPDCPDC)-3'**
	Chains	:	P
	Engineered	:	YES
	Other Details	:	DNA PRIMER STRAND
	Other Details - Source	:	PRIMER STRAND SYNTHETIC OLIGONUCLEOTIDE
	Synthetic	:	YES

*Molecule 3 - 5'-D(DAPDTPDAPDAPDCPDGPDGPDTPDTPDGPDCPDCPDCPD GPDTPDCPDTPDCPDAPDCPDTPDG)-3'*
	Chains	:	T
	Engineered	:	YES
	Other Details	:	DNA TEMPLATE STRAND
	Other Details - Source	:	TEMPLATE STRAND SYNTHETIC OLIGONUCLEOTIDE
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	P	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	DGT	1	Ligand/Ion	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2	MG	3	Ligand/Ion	MAGNESIUM ION
3	PO4	3	Ligand/Ion	PHOSPHATE ION
4	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:83 , SER A:789 , LYS A:882 , ARG A:985	BINDING SITE FOR RESIDUE PO4 A 1
2	AC2	SOFTWARE	LYS A:756 , HIS A:760 , ASN A:769 , TYR A:1020 , HIS A:1024	BINDING SITE FOR RESIDUE PO4 A 2
3	AC3	SOFTWARE	LYS A:636 , HIS A:660	BINDING SITE FOR RESIDUE PO4 A 3
4	AC4	SOFTWARE	CYS A:919 , CYS A:922 , CYS A:944 , CYS A:947	BINDING SITE FOR RESIDUE ZN A 4
5	AC5	SOFTWARE	ASP A:973 , ASP A:975 , DGT A:1456 , HOH A:1457	BINDING SITE FOR RESIDUE MG A 5
6	AC6	SOFTWARE	MG A:7 , HOH A:92 , GLU A:405 , HIS A:620 , CYS A:670	BINDING SITE FOR RESIDUE MG A 6
7	AC7	SOFTWARE	MG A:6 , HOH A:92 , HIS A:346 , HIS A:348 , GLU A:405 , ASN A:743	BINDING SITE FOR RESIDUE MG A 7
8	AC8	SOFTWARE	MG A:5 , HOH A:10 , HOH A:11 , HOH A:12 , HOH A:68 , HOH A:99 , ARG A:893 , GLY A:894 , SER A:895 , LYS A:970 , PRO A:972 , ASP A:973 , ASP A:975 , HIS A:1186 , ARG A:1213 , ARG A:1238 , TYR A:1269 , PHE A:1271 , PRO A:1272 , HIS A:1275 , HOH A:1457 , DC P:17 , DC T:5 , DG T:6	BINDING SITE FOR RESIDUE DGT A1456

(no "SS Bond" information available for 3F2B)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:847	-	Pro A:848

(no "SAP(SNP)/Variant" information available for 3F2B)

(no "PROSITE Motif" information available for 3F2B)

(no "Exon" information available for 3F2B)

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:994
 aligned with Q5L0J3_GEOKA | Q5L0J3 from UniProtKB/TrEMBL  Length:1444

    Alignment length:1212
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442  
        Q5L0J3_GEOKA    233 VRRLETIVEEERRVVVQGYVFDAEVSELKSGRTLLTMKITDYTNSILVKMFSRDKEDAELMSGVKKGMWVKVRGSVQNDTFVRDLVIIANDLNEIAANERQDTAPEGEKRVELHLHTPMSQMDAVTSVTKLIEQAKKWGHPAIAVTDHAVVQSFPEAYSAAKKHGMKVIYGLEANIVDDGVPIAYNETHRRLSEETYVVFDVETTGLSAVYNTIIELAAVKVKDGEIIDRFMSFANPGHPLSVTTMELTGITDEMVKDAPKPDEVLARFVDWAGDATLVAHNASFDIGFLNTGLARMGRGKIANPVIDTLELARFLYPDLKNHRLNTLCKKFDIELTQHHRAIYDAEATGHLLMRLLKEAEERGILFHDELNSRTHSEASYRLARPFHVTLLAQNETGLKNLFKLVSLSHIQYFHRVPRIPRSVLVKHRDGLLVGSGCDKGELFDNLIQKAPEEVEDIARFYDFLEVHPPDVYKPLIEMDYVKDEEMIKNIIRSIVALGEKLDIPVVATGNVHYLNPEDKIYRKILIHSQGGANPLNRHELPDVYFRTTNEMLDCFSFLGPEKAKEIVVDNTQKIASLIGDVKPIKDELYTPRIEGADEEIREMSYRRAKEIYGDPLPKLVEERLEKELKSIIGHGFAVIYLISHKLVKKSLDDGYLVGSRGSVGSSFVATMTEITEVNPLPPHYVCPNCKHSEFFNDGSVGSGFDLPDKNCPRCGTKYKKDGHDIPFETFLGFKGDKVPDIDLNFSGEYQPRAHNYTKVLFGEDNVYRAGTIGTVADKTAYGFVKAYASDHNLELRGAEIDRLAAGCTGVKRTTGQHPGGIIVVPDYMEIYDFTPIQYPADDTSSEWRTTHFDFHSIHDNLLKLDILGHDDPTVIRMLQDLSGIDPKTIPTDDPDVMGIFSSTEPLGVTPEQIMCNVGTIGIPEFGTRFVRQMLEETRPKTFSELVQISGLSHGTDVWLGNAQELIQNGTCTLSEVIGCRDDIMVYLIYRGLEPSLAFKIMESVRKGKGLTPEFEAEMRKHDVPEWYIDSCKKIKYMFPKAHAAAYVLMAVRIAYFKVHHPLLYYASYFTVRAEDFDLDAMIKGSAAIRKRIEEINAKGIQATAKEKSLLTVLEVALEMCERGFSFKNIDLYRSQATEFVIDGNSLIPPFNAIPGLGTNVAQAIVRAREEGEFLSKEDLQQRGKLSKTLLEYLESRGCLDSLPDHNQLSLF 1444
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh...eeeeeeeeeeeeeeeee.....eeeeeeee....eeeeeee..hhhhhhhhhh.....eeeeeeeeeee....eeeeeeeeeeee...............................hhhhhhhhhhhh....eee.......hhhhhhhhhhhhh..eeeeeeeeee..--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eeeeeee.hhhhhhhhhhhhhhhhh........eehhhhhhh...eeee...........--------...hhhhh..eee.hhhhhh..----...hhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....ee.hhhhhhhhhhhh..........eee......eee.......hhhhh............eee.....hhhhhh........eeeeee..hhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eeeeeeeeeeeee.....hhhhh..eehhhhh......eeeeehhhhh....eeeeeeehhhhhhhhhhhhhh.hhhhh...hhhhhhh...hhhhh.hhhhhh............hhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhhh...hhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.............eee..eee.hhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3f2b A  233 VRRLETIVEEERRVVVQGYVFDAEVSELKSGRTLLTMKITDYTNSILVKMFSRDKEDAELMSGVKKGMWVKVRGSVQNDTFVRDLVIIANDLNEIAANERQDTAPEGEKRVELHLHTPMSQMDAVTSVTKLIEQAKKWGHPAIAVTDHAVVQSFPEAYSAAKKHGMKVIYGLEANIVDD--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFHVTLLAQNETGLKNLFKLVSLSHIQYFHRVPRIPRSVLVKHRDGLLVGSGCDKGELFDN--------VEDIARFYDFLEVHPPDVYKPL----YVKDEEMIKNIIRSIVALGEKLDIPVVATGNVHYLNPEDKIYRKILIHSQGGANPLNRHELPDVYFRTTNEMLDCFSFLGPEKAKEIVVDNTQKIASLIGDVKPIKDELYTPRIEGADEEIREMSYRRAKEIYGDPLPKLVEERLEKELKSIIGHGFAVIYLISHKLVKKSLDDGYLVGSRGSVGSSFVATMTEITEVNPLPPHYVCPNCKHSEFFNDGSVGSGFDLPDKNCPRCGTKYKKDGHDIPFETFLGFKGDKVPDIDLNFSGEYQPRAHNYTKVLFGEDNVYRAGTIGTVADKTAYGFVKAYASDHNLELRGAEIDRLAAGCTGVKRTTGQHPGGIIVVPDYMEIYDFTPIQYPADDTSSEWRTTHFDFHSIHDNLLKLDILGHDDPTVIRMLQDLSGIDPKTIPTDDPDVMGIFSSTEPLGVTPEQIMCNVGTIGIPEFGTRFVRQMLEETRPKTFSELVQISGLSHGTDVWLGNAQELIQNGTCTLSEVIGCRDDIMVYLIYRGLEPSLAFKIMESVRKGKGLTPEFEAEMRKHDVPEWYIDSCKKIKYMFPKAHAAAYVLMAVRIAYFKVHHPLLYYASYFTVRAEDFDLDAMIKGSAAIRKRIEEINAKGIQATAKEKSLLTVLEVALEMCERGFSFKNIDLYRSQATEFVIDGNSLIPPFNAIPGLGTNVAQAIVRAREEGEFLSKEDLQQRGKLSKTLLEYLESRGCLDSLPDHNQLSLF 1444
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402        |-         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -     | 622       632       642       652       662       672     |   -    |  692       702     |   -|      722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442  
                                                                                                                                                                                                            411                                                                                                                                                                                                            618                                                         678      687                  708  713

Chain P from PDB  Type:DNA  Length:13
                                              
                3f2b P    5 GAGACGGGCAACC   17
                                    14

Chain T from PDB  Type:DNA  Length:18
                                                   
                3f2b T    1 ATAACGGTTGCCCGTCTC   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 "SCOP Domain" information available for 3F2B)

(no "CATH Domain" information available for 3F2B)

(no "Pfam Domain" information available for 3F2B)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q5L0J3_GEOKA | Q5L0J3)

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: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: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: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: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.
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
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	Cis Peptide Bonds
		Asp A:847 - Pro A:848	[ RasMol ]

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	3f2b
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3f2c	SAME PROTEIN-DNA COMPLEX CRYSTALLIZED WITH MN
3f2d	SAME PROTEIN-DNA COMPLEX CRYSTALLIZED WITH COMPLEX DGTP, MN AND ZN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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