1TFR - JenaLib

Title :   RNASE H FROM BACTERIOPHAGE T4

Authors :   T. C. Mueser, N. G. Nossal, C. C. Hyde

Date :   27 Apr 96 (Deposition) - 08 Nov 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.06

Chains :   Asym./Biol. Unit : A

Keywords :   5U-3U Exonuclease, Rna:Rna, Dna:Dna, Metal-Dependent, Magnesium-Containing, Hydrolase (Nucleic Acid) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. C. Mueser, N. G. Nossal, C. C. Hyde
Structure Of Bacteriophage T4 Rnase H, A 5' To 3' Rna-Dna And Dna-Dna Exonuclease With Sequence Similarity To The Rad2 Family Of Eukaryotic Proteins.
Cell(Cambridge, Mass. ) V. 85 1101 1996
PubMed-ID: 8674116 | Reference-DOI: 10.1016/S0092-8674(00)81310-0
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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:283
 aligned with RNH_BPT4 | P13319 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:294
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    
             RNH_BPT4    12 KEGICLIDFSQIALSTALVNFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDHIAVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLTESEYNRYKENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAGLSKLTNSINEF 305
               SCOP domains d1tfra2 A:12-180 T4 RNase H                                                                                                                                                d1tfra1 A:183-305 T4 RNase H                                                                                                SCOP domains
               CATH domains 1tfrA01 A:12-183,A:260-304 5'-nuclease                                                                                                                                      1tfrA02 A:184-259 5' to 3' exonuclease, C-terminal subdomain                1tfrA01 A:12-183,A:260-304 5'-nuclease       - CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNaseH_C-1tfrA01 A:183-305                                                                                                  Pfam domains (1)
           Pfam domains (2) ---------------5_3_exonuc_N-1tfrA02 A:27-186                                                                                                                                   ----------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeehhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....eeeee........hhhh.......---------...hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhh....eeee...hhhhh......eeee..........--.hhhhhhhhhhhh..............................hhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhh......hhhhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tfr A  12 KEGICLIDFSQIALSTALVNFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKK---------TWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDHIAVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSPMHKKWVKI--GSAEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLTESEYNRYKENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAGLSKLTNSINEF 305
                                    21        31        41        51        61        71        81      |  -      |101       111       121       131       141       151       161       171        |- |     191       201       211       221       231       241       251       261       271       281       291       301    
                                                                                                       88        98                                                                               180  |                                                                                                                          
                                                                                                                                                                                                     183

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 (2, 2)

Pfam Domains (2, 2)

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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tfr)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1tfr
		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
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RNH_BPT4 \| P13319
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.26.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description