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(-) Description

Title :  CRYSTAL STRUCTURE OF NUC COMPLEXED WITH TUNGSTATE
 
Authors :  J. A. Stuckey, J. E. Dixon
Date :  19 Oct 98  (Deposition) - 19 Oct 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Endonuclease, Phosphodiesterase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Stuckey, J. E. Dixon
Crystal Structure Of A Phospholipase D Family Member.
Nat. Struct. Biol. V. 6 278 1999
PubMed-ID: 10074947  |  Reference-DOI: 10.1038/6716

(-) Compounds

Molecule 1 - PROTEIN (ENDONUCLEASE)
    Cellular Location: PERIPLASM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Cellular Location: PERIPLASM
    Expression System Gene: NUC
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: NUC
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1WO41Ligand/IonTUNGSTATE(VI)ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1WO42Ligand/IonTUNGSTATE(VI)ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:94 , LYS A:96 , ASN A:111 , HOH A:312BINDING SITE FOR RESIDUE WO4 A 156
2ACTAUTHORHIS A:94 , LYS A:96 , ASN A:111 , WO4 A:156RESIDUES FROM BOTH MONOMERS CREATE THE ACTIVE SITE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:10 -Pro A:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BYS)

(-) 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:152
 aligned with Q46707_ECOLX | Q46707 from UniProtKB/TrEMBL  Length:177

    Alignment length:152
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  
         Q46707_ECOLX    24 EPSVQVGYSPEGSARVLVLSAIDSAKTSIRMMAYSFTAPDIMKALVAAKKRGVDVKIVIDERGNTGRASIAAMNYIANSGIPLRTDSNFPIQHDKVIIVDNVTVETGSFNFTKAAETKNSENAVVIWNMPKLAESFLEHWQDRWNQGRDYRS 175
               SCOP domains d1bysa_ A: Nuclease Nuc                                                                                                                                  SCOP domains
               CATH domains 1bysA00 A:2-153 Endonuclease Chain A                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhh..eeeee.........eeee...eeeee.....hhhhh...eeeeeee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bys A   2 EPSVQVGYSPEGSARVLVLSAIDSAKTSIRMMAYSFTAPDIMKALVAAKKRGVDVKIVIDERGNTGRASIAAMNYIANSGIPLRTDSNFPIQHDKVIIVDNVTVETGSFNFTKAAETKNSENAVVIWNMPKLAESFLEHWQDRWNQGRDYRS 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  


Chain A from PDB  Type:PROTEIN  Length:152
 aligned with Q79SE0_SALTM | Q79SE0 from UniProtKB/TrEMBL  Length:177

    Alignment length:152
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  
         Q79SE0_SALTM    24 EPSVQVGYSPEGSARVLVLSAIDSAKTSIRMMAYSFTAPDIMKALVAAKKRGVDVKIVIDERGNTGRASIAAMNYIANSGIPLRTDSNFPIQHDKVIIVDNVTVETGSFNFTKAAETKNSENAVVIWNMPKLAESFLEHWQDRWNQGRDYRS 175
               SCOP domains d1bysa_ A: Nuclease Nuc                                                                                                                                  SCOP domains
               CATH domains 1bysA00 A:2-153 Endonuclease Chain A                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhh..eeeee.........eeee...eeeee.....hhhhh...eeeeeee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bys A   2 EPSVQVGYSPEGSARVLVLSAIDSAKTSIRMMAYSFTAPDIMKALVAAKKRGVDVKIVIDERGNTGRASIAAMNYIANSGIPLRTDSNFPIQHDKVIIVDNVTVETGSFNFTKAAETKNSENAVVIWNMPKLAESFLEHWQDRWNQGRDYRS 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BYS)

(-) Gene Ontology  (3, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q46707_ECOLX | Q46707)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
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.

Chain A   (Q79SE0_SALTM | Q79SE0)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
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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  Q46707_ECOLX | Q46707
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 Related Entries

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

UniProtKB/TrEMBL
        Q46707_ECOLX | Q46707: 1byr

(-) Related Entries Specified in the PDB File

1byr