2FK6 | PR0190 - JenaLib

Title :   CRYSTAL STRUCTURE OF RNASE Z/TRNA(THR) COMPLEX

Authors :   I. Li De La Sierra-Gallay, N. Mathy, O. Pellegrini, C. Condon

Date :   04 Jan 06 (Deposition) - 21 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Protein-Trna Complex; Zinc-Dependent Metal Hydrolase; Trna Maturase, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Li De La Sierra-Gallay, N. Mathy, O. Pellegrini, C. Condon
Structure Of The Ubiquitous 3' Processing Enzyme Rnase Z Bound To Transfer Rna.
Nat. Struct. Mol. Biol. V. 13 376 2006
PubMed-ID: 16518398 | Reference-DOI: 10.1038/NSMB1066
(for further references see the PDB file header)

Compounds

Molecule 1 - TRNA(THR)
	Chains	:	R
	Engineered	:	YES
	Other Details	:	B.SUBTILIS TRNATHR(ENCODED BY THE TRN1-THR GENE) WAS TRANSCRIBED IN VITRO AS A PRECURSOR WITH 6 NT 3'-EXTENSION FROM PCR FRAGMENT GENERATED FROM PLASMID PHMT1, USING OLIGONUCLEOTIDES HP560 AND CC079
	Synthetic	:	YES

Molecule 2 - RIBONUCLEASE Z
	Chains	:	A
	EC Number	:	3.1.26.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21-CODONPLUS (LAMBDADE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RNZ
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	W168
	Synonym	:	RNASE Z; TRNASE Z; TRNA 3 ENDONUCLEASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

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 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
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Chain A from PDB  Type:PROTEIN  Length:307
 aligned with RNZ_BACSU | P54548 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:307
                                    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       
            RNZ_BACSU     1 MELLFLGTGAGIPAKARNVTSVALKLLEERRSVWLFDCGEATQHQILHTTIKPRKIEKIFITHMHGDHVYGLPGLLGSRSFQGGEDELTVYGPKGIKAFIETSLAVTKTHLTYPLAIQEIEEGIVFEDDQFIVTAVSVIHGVEAFGYRVQEKDVPGSLKADVLKEMNIPPGPVYQKIKKGETVTLEDGRIINGNDFLEPPKKGRSVVFSGDTRVSDKLKELARDCDVLVHEATFAKEDRKLAYDYYHSTTEQAAVTAKEARAKQLILTHISARYQGDASLELQKEAVDVFPNSVAAYDFLEVNVPRG 307
               SCOP domains d2fk6a1 A:1-307 Ribonuclease Z (RNase Z)                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2fk6A00 A:1-307 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.............eeeeeehhhhheeeee....hhhhhhh....hhh.eeeee....hhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhh.......eeeee...eeeee...eeeeeee.......eeeeeee.......hhhhhh.......hhhhhhhh..eee.....eee.hhhh.......eeee......hhhhhhhh....eeeee......hhhhhhhhh..hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh....eee.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fk6 A   1 MELLFLGTGAGIPAKARNVTSVALKLLEERRSVWLFDCGEATQHQMLHTTIKPRKIEKIFITHMAGDHVYGLPGLLGSRSFQGGEDELTVYGPKGIKAFIETSLAVTKTHLTYPLAIQEIEEGIVFEDDQFIVTAVSVIHGVEAFGYRVQEKDVPGSLKADVLKEMNIPPGPVYQKIKKGETVTLEDGRIINGNDFLEPPKKGRSVVFSGDTRVSDKLKELARDCDVMVHEATFAKEDRKLAYDYYHSTTEQAAVTAKEARAKQLILTHISARYQGDASLELQKEAVDVFPNSVAAYDFLEVNVPRG 307
                                    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

Chain R from PDB  Type:RNA  Length:53
                                                                                     
                 2fk6 R   1 GCUUCCAUAGCUCAGCAGGUAGAGCGUCAGCGGUUCGAGCCCGCUUGGAAGCU  73
                                    10        20    ||  50        60        70   
                                                   25|                           
                                                    46

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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (RNZ_BACSU | P54548)

molecular function
	GO:0042781	3'-tRNA processing endoribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016891	endoribonuclease activity, producing 5'-phosphomonoesters	Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0042779	tRNA 3'-trailer cleavage	Cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA; may involve endonucleolytic or exonucleolytic cleavage, or both.
	GO:0034414	tRNA 3'-trailer cleavage, endonucleolytic	Endonucleolytic cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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