2CBN - JenaLib

Title :   CRYSTAL STRUCTURE OF ZIPD FROM ESCHERICHIA COLI

Authors :   E. Pohl, W. Meyer-Klaucke, B. Kostelecky

Date :   06 Jan 06 (Deposition) - 15 Feb 06 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Phosphodiesterase Beta Lactamase Trnase Z, Hydrolase, Metal- Binding, Endonuclease, Trna Processing, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Kostelecky, E. Pohl, A. Vogel, O. Schilling, W. Meyer-Klaucke
The Crystal Structure Of The Zinc Phosphodiesterase From Escherichia Coli Provides Insight Into Function And Cooperativity Of Trnase Z-Family Proteins.
J. Bacteriol. V. 188 1607 2006
PubMed-ID: 16452444 | Reference-DOI: 10.1128/JB.188.4.1607-1614.2006

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 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:306
 aligned with RBN_ECOLI | P0A8V0 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:306
                             1                                                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299      
            RBN_ECOLI     - -MELIFLGTSAGVPTRTRNVTAILLNLQHPTQSGLWLFDCGEGTQHQLLHTAFNPGKLDKIFISHLHGDHLFGLPGLLCSRSMSGIIQPLTIYGPQGIREFVETALRISGSWTDYPLEIVEIGAGEILDDGLRKVTAYPLEHPLECYGYRIEEHDKPGALNAQALKAAGVPPGPLFQELKAGKTITLEDGRQINGADYLAAPVPGKALAIFGDTGPCDAALDLAKGVDVMVHEATLDITMEAKANSRGHSSTRQAATLAREAGVGKLIITHVSSRYDDKGCQHLLRECRSIFPATELANDFTVFNV 305
               SCOP domains -d2cbna1 A:1-305 Ribonuclease Z (RNase Z)                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2cbnA00 A:0-305 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.............eeeee........eeee....hhhhhhhh.......eeeee....hhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhh.......eeeee...eeeee...eeeeeee.......eeeeeee.......hhhhhhhh....hhhhhhhhhh...ee...ee.hhhhh........eeee........hhhhhhh...eeeee...hhhhhhhhhhh...hhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhh....eee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cbn A   0 AMNLIFLGTSAGVPTRTRNVTAILLNLQHPTQSGLWLFDCGEGTQHQLLHTAFNPGKLDKIFISHLHGDHLFGLPGLLCSRSMSGIIQPLTIYGPQGIREFVETALRISGSWTDYPLEIVEIGAGEILDDGLRKVTAYPLEHPLECYGYRIEEHDAPGALNAQALKAAGVPPGPLFQELKAGKTITLEDGRQINGADYLAAPVPGKALAIFGDTGPCDAALDLAKGVDVMVHEATLDITMEAKANSRGHSSTRQAATLAREAGVGKLIITHVSSRYDDKGCQHLLRECRSIFPATELANDFTVFNV 305
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299

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 (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (RBN_ECOLI | P0A8V0)

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:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0004532	exoribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of an RNA molecule.
	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:0090503	RNA phosphodiester bond hydrolysis, exonucleolytic	The chemical reactions and pathways involving the hydrolysis of terminal 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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