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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF A RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS AT ATOMIC RESOLUTION (1.0 A)
 
Authors :  J. Sevcik, V. S. Lamzin, Z. Dauter, K. S. Wilson
Date :  03 May 02  (Deposition) - 31 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribonuclease Sa, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sevcik, V. S. Lamzin, Z. Dauter, K. S. Wilson
Atomic Resolution Data Reveal Flexibility In The Structure Of Rnase Sa.
Acta Crystallogr. , Sect. D V. 58 1307 2002
PubMed-ID: 12136142  |  Reference-DOI: 10.1107/S0907444902010090

(-) Compounds

Molecule 1 - GUANYL-SPECIFIC RIBONUCLEASE SA
    Chains: A, B
    EC Number: 3.1.27.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEH100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: U39467
    Organism Scientific: STREPTOMYCES AUREOFACIENS
    Organism Taxid: 1894
    Synonym: RNASE SA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:62 , ARG A:63 , THR A:64 , HOH A:668 , HOH A:695 , HOH A:829 , HOH A:841 , PRO B:12 , ARG B:68BINDING SITE FOR RESIDUE SO4 A 601
2AC2SOFTWARETHR A:67 , HIS A:85 , TYR B:81 , THR B:82 , GLY B:83 , ASP B:84 , THR B:88 , PHE B:89 , SER B:90 , HOH B:631 , HOH B:643BINDING SITE FOR RESIDUE GOL B 602
3AC3SOFTWARETHR A:5 , VAL A:6 , CYS A:7 , ASP A:93 , HOH A:711 , HOH A:737 , HOH A:758 , HOH A:789 , THR B:95 , CYS B:96BINDING SITE FOR RESIDUE GOL A 603
4AC4SOFTWAREARG A:40 , GLU A:41 , TYR A:86 , HOH A:639 , HOH A:667 , HOH A:682 , HOH A:741 , HOH A:847 , GLY B:4 , THR B:5BINDING SITE FOR RESIDUE GOL A 604

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:7 -A:96
2B:7 -B:96

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:26 -Pro A:27
2Gly B:26 -Pro B:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LNI)

(-) 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:96
 aligned with RNSA_STRAU | P05798 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:96
                                    10        20        30        40        50        60        70        80        90      
            RNSA_STRAU    1 DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC 96
               SCOP domains d1lnia_ A: RNase Sa                                                                              SCOP domains
               CATH domains 1lniA00 A:1-96  [code=3.10.450.30, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.hhhhhhhhhhhhhhhh..........ee...............eeeee............eeeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  1lni A  1 DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC 96
                                    10        20        30        40        50        60        70        80        90      


Chain B from PDB  Type:PROTEIN  Length:96
 aligned with RNSA_STRAU | P05798 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:96
                                    10        20        30        40        50        60        70        80        90      
            RNSA_STRAU    1 DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC 96
               SCOP domains d1lnib_ B: RNase Sa                                                                              SCOP domains
               CATH domains 1lniB00 B:1-96  [code=3.10.450.30, no name defined]                                              CATH domains
           Pfam domains (1) ----------Ribonuclease-1lniB01 B:11-92                                                      ---- Pfam domains (1)
           Pfam domains (2) ----------Ribonuclease-1lniB02 B:11-92                                                      ---- Pfam domains (2)
         Sec.struct. author ....eee.hhhhhhhhhhhhhhhhh.........ee................eeee............eeee......eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  1lni B  1 DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC 96
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Ribonuclease] (57)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RNSA_STRAU | P05798)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid 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:0046589    ribonuclease T1 activity    Catalysis of the endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Gp with 2',3'-cyclic phosphate intermediates.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNSA_STRAU | P05798: 1ay7 1box 1c54 1gmp 1gmq 1gmr 1i70 1i8v 1rge 1rgf 1rgg 1rgh 1rsn 1sar 1t2h 1t2i 1uci 1ucj 1uck 1ucl 1ynv 1zgx 2sar 3a5e 4gho 4j5g 4j5k

(-) Related Entries Specified in the PDB File

1rgg HYDROLASE, GUANYLORIBONUCLEASE