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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE MUTANT
 
Authors :  L. Urbanikova, J. Sevcik
Date :  22 Apr 05  (Deposition) - 08 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.13
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mutant, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Urbanikova, J. Sevcik
Surface Mutation Gln To Lys Changed The Crystal Packing
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GUANYL-SPECIFIC RIBONUCLEASE SA
    Chains: A
    EC Number: 3.1.27.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-63
    Organism Scientific: STREPTOMYCES AUREOFACIENS
    Organism Taxid: 1894
    Other Details: THE PROTEIN IS CLEAVED BETWEEN ARG63 AND THR64, CHAINS A AND B REPRESENT THE TWO PARTS OF THE SAME MOLECULE
    Synonym: RNASE SA
 
Molecule 2 - GUANYL-SPECIFIC RIBONUCLEASE SA
    Chains: B
    EC Number: 3.1.27.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 64-96
    Mutation: YES
    Organism Scientific: STREPTOMYCES AUREOFACIENS
    Organism Taxid: 1894
    Other Details: THE PROTEIN IS CLEAVED BETWEEN ARG63 AND THR64, CHAINS A AND B REPRESENT THE TWO PARTS OF THE SAME MOLECULE
    Synonym: RNASE SA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:27 , PHE A:28 , GLU A:54 , HOH A:650 , ARG B:65 , ARG B:69 , HIS B:85 , TYR B:86BINDING SITE FOR RESIDUE SO4 B 601
2AC2SOFTWAREARG A:40 , PRO A:60 , GLY A:61 , ARG A:63 , HOH A:727 , HOH A:729 , HOH A:740 , HOH A:760BINDING SITE FOR RESIDUE SO4 A 602
3AC3SOFTWAREARG A:63 , GLN B:77 , ASP B:79 , LYS B:94 , HOH B:629 , HOH B:678BINDING SITE FOR RESIDUE SO4 B 603

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:26 -Pro A:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZGX)

(-) 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:63
 aligned with RNSA_STRAU | P05798 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:63
                                    10        20        30        40        50        60   
            RNSA_STRAU    1 DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGAR 63
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhhhhhhhhhhhhhh...........................eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  1zgx A  1 DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGAR 63
                                    10        20        30        40        50        60   


Chain B from PDB  Type:PROTEIN  Length:33
 aligned with RNSA_STRAU | P05798 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:33
                                    73        83        93   
            RNSA_STRAU   64 TRGTRRIITGEATQEDYYTGDHYATFSLIDQTC 96
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
           Pfam domains (1) Ribonuclease-1zgxB01 B:64-92 ---- Pfam domains (1)
           Pfam domains (2) Ribonuclease-1zgxB02 B:64-92 ---- Pfam domains (2)
         Sec.struct. author .....eeee......eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                  1zgx B 64 TRGTRRIITGEATQEDYYTGDHYATFSLIDKTC 96
                                    73        83        93
   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  (0, 0)

(no "SCOP Domain" information available for 1ZGX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZGX)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological 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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  1zgx
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  3.1.27.3
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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 1lni 1rge 1rgf 1rgg 1rgh 1rsn 1sar 1t2h 1t2i 1uci 1ucj 1uck 1ucl 1ynv 2sar 3a5e 4gho 4j5g 4j5k

(-) Related Entries Specified in the PDB File

1box N39S MUTANT
1i70 Y86F MUTANT
1i8v Y80F MUTANT
1rgg WILD TYPE OF RNASE SA
1t2h Y81W MUTANT
1t2i T76W MUTANT