2HPM - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   EUBACTERIAL AND EUKARYOTIC REPLICATIVE DNA POLYMERASES ARE NOT HOMOLOGOUS: X-RAY STRUCTURE OF DNA POLYMERASE III

Authors :   S. Bailey, R. A. Wing, T. A. Steitz

Date :   17 Jul 06 (Deposition) - 19 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.70

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

Keywords :   Nucleotidyltransferase Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bailey, R. A. Wing, T. A. Steitz
The Structure Of T. Aquaticus Dna Polymerase Iii Is Distinc From Eukaryotic Replicative Dna Polymerases.
Cell(Cambridge, Mass. ) V. 126 893 2006
PubMed-ID: 16959569 | Reference-DOI: 10.1016/J.CELL.2006.07.027

Molecule 1 - DNA POLYMERASE III ALPHA SUBUNIT
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	3PO	1	Ligand/Ion	TRIPHOSPHATE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	3PO	1	Ligand/Ion	TRIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	3PO	2	Ligand/Ion	TRIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , HIS A:47 , HIS A:214	BINDING SITE FOR RESIDUE ZN A 1221
2	AC2	SOFTWARE	HIS A:11 , HIS A:13 , HIS A:47 , GLU A:72 , ASP A:212	BINDING SITE FOR RESIDUE ZN A 1222
3	AC3	SOFTWARE	ASP A:463 , ASP A:465 , LYS A:616 , ASP A:618	BINDING SITE FOR RESIDUE MG A 1223
4	AC4	SOFTWARE	ARG A:129 , GLU A:149 , ASP A:169	BINDING SITE FOR RESIDUE MG A 1224
5	AC5	SOFTWARE	SER A:426 , ARG A:452 , ARG A:766	BINDING SITE FOR RESIDUE 3PO A 1227

(no "SS Bond" information available for 2HPM)

Asymmetric Unit

No.	Residues
1	Asp A:238	-	Pro A:239

(no "SAP(SNP)/Variant" information available for 2HPM)

(no "PROSITE Motif" information available for 2HPM)

(no "Exon" information available for 2HPM)

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:1143
 aligned with DPO3A_THEAQ | Q9XDH5 from UniProtKB/Swiss-Prot  Length:1220

    Alignment length:1201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204 
         DPO3A_THEAQ      5 LKFAHLHQHTQFSLLDGAAKLQDLLKWVKETTPEDPALAMTDHGNLFGAVEFYKKATAMGVKPIIGYEAYVAAESRFDRKRGKGLDGGYFHLTLLAKDFTGYQNLVRLASRAYLEGFYEKPRIDREILREHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIEIQNHGLPEQKKVNQVLKEFARKYGLGMVATNDGHYVRKEDARAHEVLLAIQSKTTLDDPERWRFPCDEFYVKTPEEMRAMLPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPRFPLPEGRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLLGTMPPHGDERALAEALARVEEKAWEELRKRLPPLEGVREWTAEAILHRALYELSVIERMGFPGYFLIVQDYINWARGHGVSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVIQYVRERYGEDKVAQIGTFGSLASKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQEAIQVVPELRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQEGRPVTQYDMGAVEALGLLKMDFLGLRTLTFLDEARRIVKESKGVELDYDRLPLDDPKTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHHGQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQIMQIASQVAGYSLGEADLLRRAMGKKRVEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKAHYPVEFMAALLSVERHDSDKVAEYIRDARALGIPVLPPDVNRSGFDFKVVGEEILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAFGDRARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPPLVEASPLDEITMLRYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFVRELPGKPKVLLSGMVEEVVRKPTRSGGMMARFTLSDETGALEVVVFGRAYEGVSPKLKEDIPLLVLAEVEKGEELRVLAQAVWTLEEVLEAPKALEVEVDHALLDEKGVARLKSLLDEHPGSLPVYLRVLGPFGEALFALREVRVGEEALGLLEAEGYRAYLVPDREVF 1205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhh...eeeeeee.eee.........-----..ee..eeee.hhhhhhhhhhhhhhhhhh......eehhhhhhhh...eeee.....hhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhh...hhhhhhhhhh....................--..hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..-------.hhhhhhhhh..hhhhhh.....--------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.............................eee...hhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhhh..hhhhhhhhhh...............-----.hhhhh..hhhhhhhhhhhhhhh..eeeeee...eeee...hhhhh..eee.....eeeeeehhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhh............hhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....ee...........eee..eee.........hhhhhhhhhhhhhhh....hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhh......eeeeeeee...------------..eeee..eeee..-------------....eeeeeee..-----..eeeeeeehhhhh...eeeeeee.........-hhhhhhhhh......eeeeeee..eeeeee........hhhhhhh....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2hpm A    5 LKFAHLHQHTQFSLLDGAAKLQDLLKWVKETTPEDPALAMTDHGNLFGAVEFYKKATAMGVKPIIGYEAYVAAESRFDRKR-----GGYFHLTLLAKDFTGYQNLVRLASRAYLEGFYEKPRIDREILREHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIEIQNHGLPEQKKVNQVLKEFARKYGLGMVATNDGHYVRKEDARAHEVLLAIQSKTTLDDPERWRFPCDEFYVKTPEEMRAMLPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPRFPL--GRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLL-------DERALAEALARVEEKAWEELRKR--------EWTAEAILHRALYELSVIERMGFPGYFLIVQDYINWARGHGVSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVIQYVRERYGEDKVAQIGTFGSLASKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQEA-----ELRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQEGRPVTQYDMGAVEALGLLKMDFLGLRTLTFLDEARRIVKESKGVELDYDRLPLDDPKTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHHGQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQIMQIASQVAGYSLGEADLLRRAMGKKRVEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKAHYPVEFMAALLSVERHDSDKVAEYIRDARALGIPVLPPDVNRSGFDFKVVGEEILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAFGDRARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPPLVEASPLDEITMLRYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFVRELPGKPKVLLSGMVEEV------------RFTLSDETGALEVV-------------KEDIPLLVLAEVE-----RVLAQAVWTLEEVLEAPKALEVEVDHALLDEKG-ARLKSLLDEHPGSLPVYLRVLGPFGEALFALREVRVGEEALGLLEAEGYRAYLVPDREVF 1205
                                    14        24        34        44        54        64        74        84|     | 94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     | 304       314       324       334   |     - |     354       364   |     -  |    384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534   |   544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054         -  |   1074     |   -      1094      1104 |    1114      1124      1134      1144 |    1154      1164      1174      1184      1194      1204 
                                                                                                           85    91                                                                                                                                                                                                              300  |                                338     346                   368      377                                                                                                                                                              538   544                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          1054         1067         1080          1094        1106  1112                            1144 |                                                           
                                                                                                                                                                                                                                                                                                                                    303                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1146

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 2HPM)

(no "CATH Domain" information available for 2HPM)

(no "Pfam Domain" information available for 2HPM)

Asymmetric Unit(hide GO term definitions)

Chain A (DPO3A_THEAQ | Q9XDH5)

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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		3PO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		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 ]

	Cis Peptide Bonds
		Asp A:238 - Pro A:239	[ RasMol ]

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

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Access by PDB/NDB ID
	2hpm
		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
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Access by UniProt ID/Accession number
	DPO3A_THEAQ \| Q9XDH5
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	2.7.7.7
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		Disease Information	:	OMIM

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		Interatomic Contacts of Structural Units	:	CSU
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	DPO3A_THEAQ \| Q9XDH5
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UniProtKB/Swiss-Prot
	DPO3A_THEAQ \| Q9XDH5	:	2hpi 3e0d 4iqj

2hpi	APO STRUCTURE OF POLIII ALPHA SUBUNIT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File