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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNASE Z FROM THERMOTOGA MARITIMA
 
Authors :  R. Ishii, S. Yokoyama, Riken Structural Genomics/Proteomics Init (Rsgi)
Date :  30 Dec 04  (Deposition) - 22 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metallo-Beta-Lactamase Fold, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Ishii, A. Minagawa, H. Takaku, M. Takagi, M. Nashimoto, S. Yokoyama
Crystal Structure Of The Trna 3' Processing Endoribonucleas Trnase Z From Thermotoga Maritima
J. Biol. Chem. V. 280 14138 2005
PubMed-ID: 15701599  |  Reference-DOI: 10.1074/JBC.M500355200

(-) Compounds

Molecule 1 - TRNASE Z
    Chains: A, B
    EC Number: 3.1.26.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8
    Synonym: HYPOTHETICAL PROTEIN TM0864

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:9 , ASP A:52 , ASP A:190 , HIS A:244BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREASP B:52 , ASP B:190 , HIS B:244BINDING SITE FOR RESIDUE ZN B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WW1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WW1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WW1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WW1)

(-) Exons   (0, 0)

(no "Exon" information available for 1WW1)

(-) 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:250
 aligned with Q9WZW8_THEMA | Q9WZW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:280
                                    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
         Q9WZW8_THEMA     1 MNIIGFSKALFSTWIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVVNIRNNGMGDREKPLDVFYPEGNRAVEEYTEFIKRANPDLRFSFNVHPLKEGERVFLRNAGGFKRYVQPFRTKHVSSEVSFGYHIFEVRRKLKKEFQGLDSKEISRLVKEKGRDFVTEEYHKKVLTISGDSLALDPEEIRGTELLIHECTFLDARDRRYKNHAAIDEVMESVKAAGVKKVILYHISTRYIRQLKSVIKKYREEMPDVEILYMDPRKVFEM 280
               SCOP domains d1ww1a1 A:1-280 Ribonuclease Z (RNase Z)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ww1A00 A:1-280 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeee....eee....hhhhhhhhhhhhh.eee....hhhhh.hhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeee..eeeeeeeee..---....eeeeeeeeee.-----------------------....eeeeeeeee.......hhhhhh....eeee........----...hhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh...eeee......eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ww1 A   1 MNIIGFSKALFSTWIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVVNIRNNGMGDREKPLDVFYPEGNRAVEEYTEFIKRANPDLRFSFNVHPLKEGERVFLRNAGGFKRYVQPFRTK---SEVSFGYHIFEVRRK-----------------------FVTEEYHKKVLTISGDSLALDPEEIRGTELLIHECTFLDARD----NHAAIDEVMESVKAAGVKKVILYHISTRYIRQLKSVIKKYREEMPDVEILYMDPRKVFEM 280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  |   |140       150|        -         -    |  180       190       200       210     |   -|      230       240       250       260       270       280
                                                                                                                                                              133 137           151                     175                                      216  221                                                           


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with Q9WZW8_THEMA | Q9WZW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:280
                                    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
         Q9WZW8_THEMA     1 MNIIGFSKALFSTWIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVVNIRNNGMGDREKPLDVFYPEGNRAVEEYTEFIKRANPDLRFSFNVHPLKEGERVFLRNAGGFKRYVQPFRTKHVSSEVSFGYHIFEVRRKLKKEFQGLDSKEISRLVKEKGRDFVTEEYHKKVLTISGDSLALDPEEIRGTELLIHECTFLDARDRRYKNHAAIDEVMESVKAAGVKKVILYHISTRYIRQLKSVIKKYREEMPDVEILYMDPRKVFEM 280
               SCOP domains d1ww1b_ B: Ribonuclease Z (RNase Z)                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1ww1B00 B:1-280 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) -------------------Lactamase_B_2-1ww1B01 B:20-245                                                                                                                                                                                                    ----------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------Lactamase_B_2-1ww1B02 B:20-245                                                                                                                                                                                                    ----------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee...eeeeee....eee....hhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeee..eeeeeeeee.------..eeeeeeeeee.------------------------...eeeeeeeee.......hhhhhh....eeee..------------.hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh...eeee......eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ww1 B   1 MNIIGFSKALFSTWIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVVNIRNNGMGDREKPLDVFYPEGNRAVEEYTEFIKRANPDLRFSFNVHPLKEGERVFLRNAGGFKRYVQPFRT------VSFGYHIFEVRRK------------------------VTEEYHKKVLTISGDSLALDPEEIRGTELLIHECT------------AAIDEVMESVKAAGVKKVILYHISTRYIRQLKSVIKKYREEMPDVEILYMDPRKVFEM 280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 |     140       150|        -         -     | 180       190       200       210         -  |    230       240       250       260       270       280
                                                                                                                                                             132    139         151                      176                               210          223
   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  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9WZW8_THEMA | Q9WZW8)
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: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.
biological process
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9WZW8_THEMA | Q9WZW8: 2e7y

(-) Related Entries Specified in the PDB File

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