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(-) Description

Title :  THE X-RAY STRUCTURE OF ZEBRAFISH RNASE5
 
Authors :  I. Russo Krauss, A. Merlino, F. Coscia, L. Mazzarella, F. Sica
Date :  26 Jan 10  (Deposition) - 24 Nov 10  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Angiogenins, Fish Rnases, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Pizzo, A. Merlino, M. Turano, I. Russo Krauss, F. Coscia, A. Zanfardino, M. Varcamonti, A. Furia, C. Giancola, L. Mazzarella, F. Sica, G. D'Alessio
A New Rnase Sheds Light On The Rnase/Angiogenin Subfamily From Zebrafish.
Biochem. J. V. 433 345 2010
PubMed-ID: 21050179  |  Reference-DOI: 10.1042/BJ20100892
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZEBRAFISH RNASE5
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:15 , GLN A:16 , LYS A:35 , ILE A:36 , THR A:37 , HOH A:5062BINDING SITE FOR RESIDUE ACT A 5000
2AC2SOFTWAREGLN A:16 , HIS A:17 , LYS A:45 , HIS A:117 , TYR A:118 , HOH A:5005 , HOH A:5010BINDING SITE FOR RESIDUE SO4 A 1000
3AC3SOFTWARETHR A:54 , ARG A:57 , GLN A:77 , HOH A:5006 , HOH A:5033 , HOH A:5044 , HOH A:5051 , HOH A:5064BINDING SITE FOR RESIDUE SO4 A 1001

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:84
2A:44 -A:95
3A:62 -A:110

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:92 -Pro A:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LJE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LJE)

(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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:121
 aligned with E7FH77_DANRE | E7FH77 from UniProtKB/TrEMBL  Length:130

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
         E7FH77_DANRE     2 KVPPDVDPRYQKFLRQHVDADMSVQKCDRAMSIKKITAGTGNDCKEVNTFIQATKDRITTVCGDAGTPVNNLFKSNQPFPVVTCKLKSGNRRPNCQYRGTSSTRYIVLGCDKGWPVHYDEG 122
               SCOP domains d3ljea_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh....hhhhhhhhhhhh............eeeee..hhhhhhhhhh..eeee..eeee...eeeeeeeeee.......eeeeeeeee..eeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lje A   1 KVPPDVDPRYQKFLRQHVDADMSVQKCDRAMSIKKITAGTGNDCKEVNTFIQATKDRITTVCGDAGTPVNNLFKSNQPFPVVTCKLKSGNRRPNCQYRGTSSTRYIVLGCDKGWPVHYDEG 121
                                    10        20        30        40        50        60        70        80        90       100       110       120
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LJE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LJE)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (E7FH77_DANRE | E7FH77)
molecular function
    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.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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(-) Related Entries Specified in the PDB File

2vq8 THE X-RAY STRUCTURE OF ZEBRAFISH RNASE 1
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3ljd THE X-RAY STRUCTURE OF ZEBRAFISH RNASE 1 AT PH 4.5 FROM A NEW CRYSTAL FORM
3ln8 THE X-RAY STRUCTURE OF ZF-RNASE-1 FROM A NEW CRYSTAL FORM AT PH 7.3