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(-) Description

Title :  THE X-RAY STRUCTURE OF ZF-RNASE-1 FROM A NEW CRYSTAL FORM AT PH 7.3
 
Authors :  I. Russo Krauss, A. Merlino, L. Mazzarella, F. Sica
Date :  02 Feb 10  (Deposition) - 08 Dec 10  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
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 - HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 3 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:74 , HIS A:119 , HIS A:121 , HOH A:3063 , HOH A:3217BINDING SITE FOR RESIDUE SO4 A 3000
02AC2SOFTWAREARG A:106 , TYR A:107 , HOH A:3114 , HOH A:3171 , HOH A:3416 , ARG B:66 , HOH B:3137BINDING SITE FOR RESIDUE SO4 A 3001
03AC3SOFTWAREGLY A:18 , PRO A:19 , ASP A:20 , MET A:21 , ARG A:25 , GLU A:29 , ARG A:35 , HOH A:3310 , HOH A:3328 , ARG B:58 , HOH B:3164BINDING SITE FOR RESIDUE SO4 A 3002
04AC4SOFTWARELYS A:57 , ARG A:58 , ASN A:78 , GLN A:79 , HOH A:3176BINDING SITE FOR RESIDUE SO4 A 3004
05AC5SOFTWAREASN A:73 , LYS A:111 , HOH A:3417 , GLU B:7 , LYS B:10BINDING SITE FOR RESIDUE SO4 A 3006
06AC6SOFTWAREASN A:27 , GLU A:98 , HOH A:3022 , HOH A:3069 , ARG B:106 , TYR B:107 , HOH B:3066 , HOH B:3072 , HOH B:3392BINDING SITE FOR RESIDUE SO4 B 3003
07AC7SOFTWAREGLU A:7 , LYS A:10 , ARG B:100 , HOH B:3028 , HOH B:3119 , HOH B:3196 , HOH B:3364BINDING SITE FOR RESIDUE SO4 B 3005
08AC8SOFTWAREASP A:123 , GLU A:124 , HOH A:3307 , HOH A:3311 , GLU B:114 , HOH B:3100 , HOH B:3341 , HOH B:3436BINDING SITE FOR RESIDUE SO4 B 3007
09AC9SOFTWAREMET A:3 , ASN A:126 , LYS B:6 , ASP B:43 , ASN B:44 , ARG B:93 , HOH B:3116 , HOH B:3337 , HOH B:3422BINDING SITE FOR RESIDUE SO4 B 3008
10BC1SOFTWAREHOH A:3305 , GLY B:18 , PRO B:19 , ASP B:20 , MET B:21 , ARG B:25 , GLU B:29 , ARG B:35 , HOH B:3334 , HOH B:3355BINDING SITE FOR RESIDUE SO4 B 3009

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:26 -A:86
2A:46 -A:97
3A:64 -A:112
4B:26 -B:86
5B:46 -B:97
6B:64 -B:112

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:94 -Pro A:95
2His B:94 -Pro B:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LN8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LN8)

(-) Exons   (0, 0)

(no "Exon" information available for 3LN8)

(-) 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:126
 aligned with E7FH76_DANRE | E7FH76 from UniProtKB/TrEMBL  Length:126

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
         E7FH76_DANRE     1 MHVKERYKNFLNQHVGPDMSVQRCNSEIGPNNRKITLSGTDNGCKPVNTFILANKRLIKTVCGRAGSPQGNMVRSNQPFPVVKCVLNNGERHPYCEYRGTRSTRYIVLKCEEGWPVHYHEDEVNVG 126
               SCOP domains d3ln8a_ A: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhh.................eeeee..hhhhhhhhhh..eeee..eeee...eeeeeeeeee.......eeeeeeeee..eeeee..eeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ln8 A   3 MHVKERYKNFLNQHVGPDMSVQRCNSEIGPNNRKITLSGTDNGCKPVNTFILANKRLIKTVCGRAGSPQGNMVRSNQPFPVVKCVLNNGERHPYCEYRGTRSTRYIVLKCEEGWPVHYHEDEVNVG 128
                                    12        22        32        42        52        62        72        82        92       102       112       122      


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with E7FH76_DANRE | E7FH76 from UniProtKB/TrEMBL  Length:126

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
         E7FH76_DANRE     1 MHVKERYKNFLNQHVGPDMSVQRCNSEIGPNNRKITLSGTDNGCKPVNTFILANKRLIKTVCGRAGSPQGNMVRSNQPFPVVKCVLNNGERHPYCEYRGTRSTRYIVLKCEEGWPVHYHEDEVNVG 126
               SCOP domains d3ln8b_ B: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhh.................eeeee..hhhhhhhhhh..eeee..eeee...eeeeeeeeee.......eeeeeeeee..eeeee..eeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ln8 B   3 MHVKERYKNFLNQHVGPDMSVQRCNSEIGPNNRKITLSGTDNGCKPVNTFILANKRLIKTVCGRAGSPQGNMVRSNQPFPVVKCVLNNGERHPYCEYRGTRSTRYIVLKCEEGWPVHYHEDEVNVG 128
                                    12        22        32        42        52        62        72        82        92       102       112       122
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LN8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LN8)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (E7FH76_DANRE | E7FH76)
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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        E7FH76_DANRE | E7FH76: 3ljd

(-) Related Entries Specified in the PDB File

2vq8 THE X-RAY STRUCTURE OF ZEBRAFISH RNASE 1
2vq9 THE X-RAY STRUCTURE OF ZEBRAFISH RNASE 3
3ljd THE X-RAY STRUCTURE OF ZEBRAFISH RNASE 1 AT PH 4.5 FROM A NEW CRYSTAL FORM
3lje THE X-RAY STRUCTURE OF ZEBRAFISH RNASE5