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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT V66Q/P117G/H124L/S128A AT 100 K
 
Authors :  J. L. Schlessman, C. Abe, E. B. Garcia-Moreno
Date :  18 May 07  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Staphylococcal Nuclease, Nuclease, Hyperstable Variant, Internal Waters, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Schlessman, C. Abe, A. Gittis, D. A. Karp, M. A. Dolan, E. B. Garcia-Moreno
Crystallographic Study Of Hydration Of An Internal Cavity In Engineered Proteins With Buried Polar Or Ionizable Groups.
Biophys. J. V. 94 3208 2008
PubMed-ID: 18178652  |  Reference-DOI: 10.1529/BIOPHYSJ.107.122473
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THERMONUCLEASE
    Chains: A
    EC Number: 3.1.31.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: LAMBDA
    Expression System Strain: AR120
    Expression System Vector Type: PLASMID
    Gene: NUC
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Synonym: TNASE, MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:35 , LYS A:71 , ARG A:87 , HOH A:317BINDING SITE FOR RESIDUE PO4 A 251

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PZT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PZT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PZT)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNASE_3PS50830 Thermonuclease domain profile.NUC_STAAW87-221  1A:8-141
2TNASE_1PS01123 Thermonuclease family signature 1.NUC_STAAW98-122  1A:19-43
3TNASE_2PS01284 Thermonuclease family signature 2.NUC_STAAW162-172  1A:83-93

(-) Exons   (0, 0)

(no "Exon" information available for 2PZT)

(-) 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:130
 aligned with A5A523_STAAU | A5A523 from UniProtKB/TrEMBL  Length:215

    Alignment length:135
                                    84        94       104       114       124       134       144       154       164       174       184       194       204     
         A5A523_STAAU    75 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQLLRKSEAQAKKEKLNIWS 209
               SCOP domains d2pzta_ A: Staphylococcal nuclease                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------SNase-2pztA01      A:33-141                                                                                   Pfam domains
         Sec.struct. author ..eeeeeeeee....eeeeee..eeeeeee..ee.....-----...hhhhhhhhhhhhhhhh..eeeee...........eeeeeee..eehhhhhhhh...ee.........hhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzt A   7 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETK-----VEKYGPEASAFTKKMQENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWS 141
                                    16        26        36        |-    |   56        66        76        86        96       106       116       126       136     
                                                                 45    51                                                                                          


Chain A from PDB  Type:PROTEIN  Length:130
 aligned with NUC_STAAW | Q8NXI6 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:135
                                    95       105       115       125       135       145       155       165       175       185       195       205       215     
            NUC_STAAW    86 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQLLRKSEAQAKKEKLNIWS 220
               SCOP domains d2pzta_ A: Staphylococcal nuclease                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------SNase-2pztA01      A:33-141                                                                                   Pfam domains
         Sec.struct. author ..eeeeeeeee....eeeeee..eeeeeee..ee.....-----...hhhhhhhhhhhhhhhh..eeeee...........eeeeeee..eehhhhhhhh...ee.........hhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TNASE_3  PDB: A:8-141 UniProt: 87-221                                                                                                  PROSITE (1)
                PROSITE (2) ------------TNASE_1  PDB: A:19-43    ---------------------------------------TNASE_2    ------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzt A   7 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETK-----VEKYGPEASAFTKKMQENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWS 141
                                    16        26        36        |-    |   56        66        76        86        96       106       116       126       136     
                                                                 45    51
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PZT)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SNase] (72)

(-) Gene Ontology  (7, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A5A523_STAAU | A5A523)
molecular function
    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.

Chain A   (NUC_STAAW | Q8NXI6)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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
        NUC_STAAW | Q8NXI6: 2gsi 2lkv 2m00 2oxp 2pqe 2pw5 2pw7 2pyk 2pzu 2pzw 3d4w 3d8g 3mvv 3qoj 3qol 3qon 3r3o
UniProtKB/TrEMBL
        A5A523_STAAU | A5A523: 2f3v 2kq3 2pzu

(-) Related Entries Specified in the PDB File

1u9r 2pw5 2pw7 2pyk 2pzu 2pzw