2XHB - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS IN COMPLEX WITH HYPOXANTHINE-CONTAINING DNA

Authors :   T. Killelea, S. Ghosh, S. S. Tan, P. Heslop, S. J. Firbank, E. T. Kool, B. A. Connolly

Date :   14 Jun 10 (Deposition) - 21 Jul 10 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.72

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

Keywords :   Transferase-Dna Complex, Replication, Exonuclease, Dna Damage, Exo Minus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Killelea, S. Ghosh, S. S. Tan, P. Heslop, S. J. Firbank, E. T. Kool, B. A. Connolly
Probing The Interaction Of Archaeal Dna Polymerases With Deaminated Bases Using X-Ray Crystallography And Non-Hydrogen Bonding Isosteric Base Analogues.
Biochemistry V. 49 5772 2010
PubMed-ID: 20527806 | Reference-DOI: 10.1021/BI100421R

Molecule 1 - DNA POLYMERASE
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	THERMOCOCCUS GORGONARIUS
	Organism Taxid	:	71997
	Synonym	:	TO POL

Molecule 2 - HYPOXANTHINE-CONTAINING DNA
	Chains	:	D
	Synthetic	:	YES

*Molecule 3 - 5'-D(APAPAPAPAPAPAPAPA)-3'**
	Chains	:	E
	Synthetic	:	YES

		1	2	3
Asymmetric Unit	:	A	D	E
Biological Unit 1 (1x)	:	A	D
Biological Unit 2 (1x)	:			E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:101 , HIS A:103 , VAL A:106 , HOH A:2005 , HOH A:2006	BINDING SITE FOR RESIDUE NA A1758

Asymmetric Unit

No.	Residues
1	A:506	-	A:509

(no "Cis Peptide Bond" information available for 2XHB)

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

Asymmetric 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_THEGO	538-546	1	A:538-546

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL_THEGO	538-546	1	A:538-546

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL_THEGO	538-546	0	-

(no "Exon" information available for 2XHB)

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:741
 aligned with DPOL_THEGO | P56689 from UniProtKB/Swiss-Prot  Length:773

    Alignment length:757
                                    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       
           DPOL_THEGO     1 MILDTDYITEDGKPVIRIFKKENGEFKIDYDRNFEPYIYALLKDDSAIEDVKKITAERHGTTVRVVRAEKVKKKFLGRPIEVWKLYFTHPQDVPAIRDKIKEHPAVVDIYEYDIPFAKRYLIDKGLIPMEGDEELKMLAFDIETLYHEGEEFAEGPILMISYADEEGARVITWKNIDLPYVDVVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFDFAYLKKRSEKLGVKFILGREGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLERVARYSMEDAKVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLNREGCEEYDVAPQVGHKFCKDFPGFIPSLLGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYAVIDEEDKITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDYKATGPHVAVAKRLAARGIKIRPGTVISYIVLKGSGRIGDRAIPFDEFDPAKHKYDAEYYIENQVLPAVERILRAFGYRKEDLRY 757
               SCOP domains d2xhba1 A:1-347 automated matches                                                                                                                                                                                                                                                                                                                          d2xhba2 A:348-757 automate           d matches                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..eeeeeeeeee..eeeeeee.....eeeeee.hhhhhhhhhh.eeee..eeee..eeeeeeee....eeeeeeee....hhhhhhhhhhhhh..eeeee....hhhhhhhhhh............eeeeeeee.-----......eeeeeeee..eeeeee........eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh............eeeee..eeeee....eeeehhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhh.........-----------............eeeeeeee..hhhhhhhhhh..hhhh........eee......eee....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...eeeee....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee..eeeee.....eeee.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhheeee...hhhhh...hhhhhhhhhhhhh........eeeeee.....hhhhheee...........hhhhhhhhhhhhhhhhhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhb A   1 MILDTDYITEDGKPVIRIFKKENGEFKIDYDRNFEPYIYALLKDDSAIEDVKKITAERHGTTVRVVRAEKVKKKFLGRPIEVWKLYFTHPQDVPAIRDKIKEHPAVVDIYEYDIPFAKRYLIDKGLIPMEGDEELKMLAFDIETL-----EFAEGPILMISYADEEGARVITWKNIDLPYVDVVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFILGREGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLERVARYSMEDAKVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPD-----------AGGYVKEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLNREGCEEYDVAPQVGHKFCKDFPGFIPSLLGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYAVIDEEDKITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDYKATGPHVAVAKRLAARGIKIRPGTVISYIVLKGSGRIGDRAIPFDEFDPAKHKYDAEYYIENQVLPAVERILRAFGYRKEDLRY 757
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    |    -|      160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370  |      -    |  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       
                                                                                                                                                                          145   151                                                                                                                                                                                                                           373         385

Chain D from PDB  Type:DNA  Length:20
                                                    
                 2xhb D   2 IGGAGACACGGCCGTGTCTC  27
                                    11 ||     27
                                      13|       
                                       20

Chain E from PDB  Type:DNA  Length:9
                                         
                 2xhb E   1 AAAAAAAAA   9

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 2XHB)

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

Asymmetric Unit(hide GO term definitions)

Chain A (DPOL_THEGO | P56689)

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: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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xhb)

Biological Units
	Complete Structure
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	2xhb
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	2.7.7.7
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UniProtKB/Swiss-Prot
	DPOL_THEGO \| P56689	:	1tgo 2vwj 2vwk

1tgo	THERMOSTABLE B TYPE DEOXYRIBONUCLEIC ACID POLYMERASE FROM THERMOCOCCUS GORGONARIUS
1wn7	CRYSTAL STRUCTURE OF ARCHAEAL FAMILY B DNA POLYMERASE MUTANT
2vwj	URACIL RECOGNITION IN ARCHAEAL DNA POLYMERASES CAPTURED BY X-RAY CRYSTALLOGRAPHY.
2vwk	URACIL RECOGNITION IN ARCHAEAL DNA POLYMERASES CAPTURED BY X-RAY CRYSTALLOGRAPHY. V93Q POLYMERASE VARIANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

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 (0, 0)

Gene Ontology (15, 15)

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