2XY8 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   PARAMAGNETIC-BASED NMR STRUCTURE OF THE COMPLEX BETWEEN THE N-TERMINAL EPSILON DOMAIN AND THE THETA DOMAIN OF THE DNA POLYMERASE III

Authors :   C. Schmitz, A. M. J. J. Bonvin

Date :   16 Nov 10 (Deposition) - 29 Jun 11 (Release) - 03 Aug 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (10x)
NMR Structure *: A,B  (1x)

Keywords :   Transferase, Docking, Experimental Restraints, Haddock Program (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Schmitz, A. M. J. J. Bonvin
Protein-Protein Haddocking Using Exclusively Pseudocontact Shifts.
J. Biomol. Nmr V. 50 263 2011
PubMed-ID: 21626213 | Reference-DOI: 10.1007/S10858-011-9514-4
(for further references see the PDB file header)

Molecule 1 - DNA POLYMERASE III SUBUNIT EPSILON
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	EXONUCLEASE DOMAIN, RESIDUES 1-186
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - DNA POLYMERASE III SUBUNIT THETA
	Chains	:	B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
NMR Structure (10x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION

NMR Structure * (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:12 , GLU A:14 , ASP A:167	BINDING SITE FOR RESIDUE CA A 190

(no "SS Bond" information available for 2XY8)

(no "Cis Peptide Bond" information available for 2XY8)

(no "SAP(SNP)/Variant" information available for 2XY8)

(no "PROSITE Motif" information available for 2XY8)

(no "Exon" information available for 2XY8)

NMR Structure

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:175
 aligned with DPO3E_ECOLI | P03007 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     
          DPO3E_ECOLI     7 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGG 181
               SCOP domains d2xy8a_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --RNase_T-2xy8A01 A:9-175                                                                                                                                                ------ Pfam domains
         Sec.struct. author .eeeeeeee..............eeeeeeeeee..ee....eeee.......hhhhhhhhh.hhhhh........hhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh.....hhhhh.eeeehhhhhhhhh.....hhhhhhhhh..........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xy8 A   7 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGG 181
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain B from PDB  Type:PROTEIN  Length:61
 aligned with HOLE_ECO57 | P0ABT0 from UniProtKB/Swiss-Prot  Length:76

    Alignment length:61
                                    19        29        39        49        59        69 
           HOLE_ECO57    10 QTEMDKVNVDLAAAGVAFKERYNMPVIAEAVEREQPEHLRSWFRERLIAHRLASVNLSRLP  70
               SCOP domains d2xy8b_ B: Theta subunit of DNA polymerase III                SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains DNA_pol3_theta-2xy8B01 B:10-70                                Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 2xy8 B  10 QTEMDKVNVDLAAAGVAFKERYNMPVIAEAVEREQPEHLRSWFRERLIAHRLASVNLSRLP  70
                                    19        29        39        49        59        69

Chain B from PDB  Type:PROTEIN  Length:61
 aligned with HOLE_ECOLI | P0ABS8 from UniProtKB/Swiss-Prot  Length:76

    Alignment length:61
                                    19        29        39        49        59        69 
           HOLE_ECOLI    10 QTEMDKVNVDLAAAGVAFKERYNMPVIAEAVEREQPEHLRSWFRERLIAHRLASVNLSRLP  70
               SCOP domains d2xy8b_ B: Theta subunit of DNA polymerase III                SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains DNA_pol3_theta-2xy8B01 B:10-70                                Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 2xy8 B  10 QTEMDKVNVDLAAAGVAFKERYNMPVIAEAVEREQPEHLRSWFRERLIAHRLASVNLSRLP  70
                                    19        29        39        49        59        69

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 2XY8)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RNase_H (288)

Family: RNase_T (14)

Escherichia coli (strain K12) (6)

RNase_T-2xy8A01

A:9-175

Clan: no clan defined [family: DNA_pol3_theta] (2)

Family: DNA_pol3_theta (2)

Escherichia coli O157:H7 (1)

DNA_pol3_theta-2xy8B01

B:10-70

NMR Structure(hide GO term definitions)

Chain A (DPO3E_ECOLI | P03007)

molecular function
	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: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: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: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:0045004	DNA replication proofreading	Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity.
	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:0044776	DNA polymerase III, core complex	The DNA polymerase III core complex consists of the alpha,epsilon and theta subunits and is carries out the polymerase and the 3'-5' exonuclease proofreading activities.

Chain B (HOLE_ECOLI | P0ABS8)

molecular function
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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: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.
cellular component
	GO:0044776	DNA polymerase III, core complex	The DNA polymerase III core complex consists of the alpha,epsilon and theta subunits and is carries out the polymerase and the 3'-5' exonuclease proofreading activities.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B (HOLE_ECO57 | P0ABT0)

molecular function
	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: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.

NMR Structure
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1j53	STRUCTURE OF THE N-TERMINAL EXONUCLEASE DOMAIN OF THEEPSILON SUBUNIT OF E.COLI DNA POLYMERASE III AT PH 8.5
1j54	STRUCTURE OF THE N-TERMINAL EXONUCLEASE DOMAIN OF THEEPSILON SUBUNIT OF E.COLI DNA POLYMERASE III AT PH 5.8
1mgz	MODEL FOR THE CATALYTIC DOMAIN OF THE PROOFREADING EPSILONSUBUNIT OF E. COLI DNA POLYMERASE III BASED ON NMRSTRUCTURAL DATA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

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Pfam Domains (2, 2)

Gene Ontology (16, 30)

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