2IHN - JenaLib

Title :   CO-CRYSTAL OF BACTERIOPHAGE T4 RNASE H WITH A FORK DNA SUBSTRATE

Authors :   J. M. Devos, T. C. Mueser

Date :   26 Sep 06 (Deposition) - 21 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A,C,D

Keywords :   Bpt4 Rnase H, Protein:Dna Complex, 5'-3' Exonuclease, Hydrolase (Nucleic Acid), Helix-Hairpin-Helix Motif Type 2 (Hhh2), Fork Dna, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Devos, S. J. Tomanicek, C. E. Jones, N. G. Nossal, T. C. Mueser
Crystal Structure Of Bacteriophage T4 5' Nuclease In Complex With A Branched Dna Reveals How Fen-1 Family Nucleases Bind Their Substrates.
J. Biol. Chem. V. 282 31713 2007
PubMed-ID: 17693399 | Reference-DOI: 10.1074/JBC.M703209200
(for further references see the PDB file header)

Compounds

*Molecule 1 - 5'- D(CPTPAPAPCPTPTPTPGPAPGPGPCPAPGPAPCPC)- 3'*
	Chains	:	C
	Engineered	:	YES
	Other Details	:	DNA WAS DESIGNED ACCORDING TO SEQUENCES IN HARRINGTON, J.J. AND LIEBER, M.R. EMBO J. 13, 1235-46 (1994)
	Synthetic	:	YES

*Molecule 2 - 5'- D(GPGPTPCPTPGPCPCPTPCPAPAPGPAPCPGPGPTPAP GPTPCPAPA)-3'*
	Chains	:	D
	Engineered	:	YES
	Other Details	:	DNA WAS DESIGNED ACCORDING TO SEQUENCES IN HARRINGTON, J.J. AND LIEBER, M.R. EMBO J. 13, 1235-46 (1994)
	Synthetic	:	YES

Molecule 3 - RIBONUCLEASE H
	Chains	:	A
	EC Number	:	3.1.26.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNN2202-D132N
	Expression System Strain	:	BL21(DE3)-PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RNH, 33.2, DAS
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665
	Strain	:	T4D
	Synonym	:	RNASE H

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:299
 aligned with RNH_BPT4 | P13319 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:305
                                    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     
             RNH_BPT4     1 MDLEMMLDEDYKEGICLIDFSQIALSTALVNFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDHIAVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLTESEYNRYKENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAGLSKLTNSINEF 305
               SCOP domains -----------d2ihna2 A:12-180 T4 RNase H                                                                                                                                              --d2ihna1 A:183-305 T4 RNase H                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhh.......------...hhhhhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh..eeee.............hhhhhhhhhhhhh............................hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh........hhhhhhhhh.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ihn A   1 MDLEMMLDEDYKEGICLIDFSQIALSTALVNFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKKNR------STWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEANDHIAVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLTESEYNRYKENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAGLSKLTNSINEF 305
                                    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     
                                                                                                                    90     97

Chain C from PDB  Type:DNA  Length:17
                                                 
                 2ihn C   2 TAACTTTGAGGCAGACC  18
                                    11

Chain D from PDB  Type:DNA  Length:17
                                                 
                 2ihn D   1 GGTCTGCCTCAAGACGG  17
                                    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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RNH_BPT4 | P13319)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	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:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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.
biological process
	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:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	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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	3.1.26.4
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