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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE Z
 
Authors :  I. L. De La Sierra-Gallay, O. Pellegrini, C. Condon
Date :  30 Nov 04  (Deposition) - 25 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Zinc-Dependent Metal Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. L. De La Sierra-Gallay, O. Pellegrini, C. Condon
Structural Basis For Substrate Binding, Cleavage And Allostery In The Trna Maturase Rnase Z.
Nature V. 433 657 2005
PubMed-ID: 15654328  |  Reference-DOI: 10.1038/NATURE03284
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE Z
    Chains: A, B
    EC Number: 3.1.26.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 LAMBDADE3 PRIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNZ
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: RNASE Z, TRNA 3 ENDONUCLEASE, ZIPD, 3'TRNASE, ELAC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MSE9Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION
5ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:63 , HIS A:65 , HIS A:140 , ASP A:211 , ZN A:401 , PO4 A:945 , HOH A:1007BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWAREASP A:67 , HIS A:68 , ASP A:211 , HIS A:269 , ZN A:400 , PO4 A:945 , HOH A:1007BINDING SITE FOR RESIDUE ZN A 401
3AC3SOFTWAREGLY A:11 , HIS A:65 , ASP A:67 , HIS A:140 , ASP A:211 , HIS A:247 , HIS A:269 , ZN A:400 , ZN A:401 , HOH A:948 , HOH A:1007BINDING SITE FOR RESIDUE PO4 A 945
4AC4SOFTWAREARG B:31 , ARG B:54 , LYS B:55 , GLU B:57 , ASP B:86 , HOH B:859BINDING SITE FOR RESIDUE MES B 801
5AC5SOFTWARELYS B:176 , VAL B:183 , THR B:184 , PRO B:291 , ASN B:292 , HOH B:861BINDING SITE FOR RESIDUE GOL B 601
6AC6SOFTWAREHIS A:48 , PHE A:299BINDING SITE FOR RESIDUE GOL A 602
7AC7SOFTWAREARG A:31 , ARG A:54 , LYS A:55 , ILE A:56 , GLU A:57 , ARG A:79 , ASP A:86 , GLU A:87 , HOH A:983BINDING SITE FOR RESIDUE GOL A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y44)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y44)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y44)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y44)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y44)

(-) 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:269
 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 d1y44a1 A:1-307 Ribonuclease Z (RNase Z)                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -1y44A00 A:2-307 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.............eeeee.......eeee....hhhhhhh....hhh.eeeee....hhhhh.hhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhh.......eeeee...eeeee...eeeeeee.......eeeeeee.......--------------------------------------........eeee......hhhhhhhh....eeeee......hhhhhhhh...hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh..eee.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y44 A   1 mELLFLGTGAGIPAKARNVTSVALKLLEERRSVWLFDCGEATQHQmLHTTIKPRKIEKIFITHmHGDHVYGLPGLLGSRSFQGGEDELTVYGPKGIKAFIETSLAVTKTHLTYPLAIQEIEEGIVFEDDQFIVTAVSVIHGVEAFGYRVQEKDVPGSL--------------------------------------LEPPKKGRSVVFSGDTRVSDKLKELARDCDVmVHEATFAKEDRKLAYDYYHSTTEQAAVTAKEARAKQLILTHISARYQGDASLELQKEAVDVFPNSVAAYDFLEVNVPRG 307
                            |       10        20        30        40     |  50        60   |    70        80        90       100       110       120       130       140       150       | -         -         -         -      |200       210       220       230       240       250       260       270       280       290       300       
                            |                                           46-MSE            64-MSE                                                                                       158                                    197                            228-MSE                                                                           
                            1-MSE                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:297
 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 d1y44b_ B: Ribonuclease Z (RNase Z)                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1y44B00 B:2-307 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) -------------------------------Lactamase_B_2-1y44B01 B:32-270                                                                                                                                                                                                                 ------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------Lactamase_B_2-1y44B02 B:32-270                                                                                                                                                                                                                 ------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee.............eeeeeehhhhheeeee....hhhhhhh....hhh.eeeee....hhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhh.......eeeee...eeeee...eeeeeee.......eeeeeee.......hhhhhhhh....hhhhhhhhh..eee.....eee.hhhh.......eeee......hhhhhhhh....eeeee.....----------.hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhh....eee.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y44 B   1 mELLFLGTGAGIPAKARNVTSVALKLLEERRSVWLFDCGEATQHQmLHTTIKPRKIEKIFITHmHGDHVYGLPGLLGSRSFQGGEDELTVYGPKGIKAFIETSLAVTKTHLTYPLAIQEIEEGIVFEDDQFIVTAVSVIHGVEAFGYRVQEKDVPGSLKADVLKEmNIPPGPVYQKIKKGETVTLEDGRIINGNDFLEPPKKGRSVVFSGDTRVSDKLKELARDCDVmVHEATFAK----------HSTTEQAAVTAKEARAKQLILTHISARYQGDASLELQKEAVDVFPNSVAAYDFLEVNVPRG 307
                            |       10        20        30        40     |  50        60   |    70        80        90       100       110       120       130       140       150       160     | 170       180       190       200       210       220       230     |   -      |250       260       270       280       290       300       
                            1-MSE                                       46-MSE            64-MSE                                                                                               166-MSE                                                       228-MSE 236        247
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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        RNZ_BACSU | P54548: 2fk6 4gcw

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