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(-) Description

Title :  CRYSTAL STRUCTURE COMPLEX OF NUCLEASE A (NUCA) WITH INTRA-CELLULAR INHIBITOR NUIA
 
Authors :  M. Ghosh, G. Meiss, A. M. Pingoud, R. E. London, L. C. Pedersen
Date :  01 Dec 06  (Deposition) - 19 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nuclease, Nuclease Inhibitor, Metal Complex, Non-Specific Nuclease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ghosh, G. Meiss, A. M. Pingoud, R. E. London, L. C. Pedersen
The Nuclease A-Inhibitor Complex Is Characterized By A Nove Metal Ion Bridge.
J. Biol. Chem. V. 282 5682 2007
PubMed-ID: 17138564  |  Reference-DOI: 10.1074/JBC.M605986200

(-) Compounds

Molecule 1 - NUCLEASE
    Chains: A
    EC Number: 3.1.30.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NUCA
    Mutation: YES
    Organism Scientific: NOSTOC SP.
    Organism Taxid: 103690
    Strain: PCC 7120
    Synonym: ENDONUCLEASE
 
Molecule 2 - SUGAR-NON-SPECIFIC NUCLEASE INHIBITOR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NUIA
    Organism Scientific: NOSTOC SP.
    Organism Taxid: 103690
    Strain: PCC 7120

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MG1Ligand/IonMAGNESIUM ION
3NI2Ligand/IonNICKEL (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:246 , GLU A:249 , GLU A:269 , HOH A:933 , HOH A:1081 , ASP B:79BINDING SITE FOR RESIDUE NI A 301
2AC2SOFTWAREGLU A:249 , ASP A:255 , PHE A:256 , GLN A:265 , GLU A:269 , ASP B:79BINDING SITE FOR RESIDUE NI A 302
3AC3SOFTWAREASN A:155 , HOH A:902 , HOH A:977 , HOH A:978 , HOH A:979 , THR B:135BINDING SITE FOR RESIDUE MG A 303
4AC4SOFTWAREGLU A:92 , GLN A:94 , HOH A:1076 , VAL B:61 , PHE B:66 , ARG B:69 , ARG B:106BINDING SITE FOR RESIDUE MES A 900
5AC5SOFTWAREARG A:156 , GLY A:160 , ASP A:164 , GLU B:109 , VAL B:110 , THR B:135BINDING SITE FOR RESIDUE MES A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O3B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O3B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O3B)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUCLEASE_NON_SPECPS01070 DNA/RNA non-specific endonucleases active site.NUCA_NOSS1121-129  1A:122-129

(-) Exons   (0, 0)

(no "Exon" information available for 2O3B)

(-) 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:241
 aligned with NUCA_NOSS1 | P38446 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:241
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273 
           NUCA_NOSS1    34 PSISVHLLLGNPSGATPTKLTPDNYLMVKNQYALSYNNSKGTANWVAWQLNSSWLGNAERQDNFRPDKTLPAGWVRVTPSMYSGSGYDRGHIAPSADRTKTTEDNAATFLMTNMMPQTPDNNRNTWGNLEDYCRELVSQGKELYIVAGPNGSLGKPLKGKVTVPKSTWKIVVVLDSPGSGLEGITANTRVIAVNIPNDPELNNDWRAYKVSVDELESLTGYDFLSNVSPNIQTSIESKVDN 274
               SCOP domains -d2o3ba1 A:35-274 Nuclease NucA                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------Endonuclease_NS-2o3bA01 A:61-263                                                                                                                                                                           ----------- Pfam domains
         Sec.struct. author ...hhhhh................eeee....eeeee....eeeeeeeeehhhhh......................hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....hhhhh.....eeeeeeeee....hhhhhh....eeeeeeee.......hhhhhh.hhhhhhhhhh.......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o3b A  34 GSISVHLLLGNPSGATPTKLTPDNYLMVKNQYALSYNNSKGTANWVAWQLNSSWLGNAERQDNFRPDKTLPAGWVRVTPSMYSGSGYARGHIAPSADRTKTTEDNAATFLMTNMMPQTPDNNRNTWGNLEDYCRELVSQGKELYIVAGPNGSLGKPLKGKVTVPKSTWKIVVVLDSPGSGLEGITANTRVIAVNIPNDPELNNDWRAYKVSVDELESLTGYDFLSNVSPNIQTSIESKVDN 274
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273 


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with Q7A260_NOSS1 | Q7A260 from UniProtKB/TrEMBL  Length:135

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
         Q7A260_NOSS1     1 MTKTNSEILEQLKQASDGLLFMSESEYPFEVFLWEGSAPPVTHEIVLQQTGHGQDAPFKVVDIDSFFSRATTPQDWYEDEENAVVAKFQKLLEVIKSNLKNPQVYRLGEVELDVYVIGETPAGNLAGISTKVVET 135
               SCOP domains d2o3bb_ B: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -NuiA-2o3bB01 B:2-135                                                                                                                   Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh...ee...ee..eeeee.......hhhhhhhhhh......eeeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhheeeeeeee...eeeeeeeee.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o3b B   1 STKTNSEILEQLKQASDGLLFMSESEYPFEVFLWEGSAPPVTHEIVLQQTGHGQDAPFKVVDIDSFFSRATTPQDWYEDEENAVVAKFQKLLEVIKSNLKNPQVYRLGEVELDVYVIGETPAGNLAGISTKVVET 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O3B)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: His-Me_finger (38)
(-)
Clan: no clan defined [family: NuiA] (2)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NUCA_NOSS1 | P38446)
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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain B   (Q7A260_NOSS1 | Q7A260)

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  Q7A260_NOSS1 | Q7A260
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 Related Entries

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

UniProtKB/Swiss-Prot
        NUCA_NOSS1 | P38446: 1zm8
UniProtKB/TrEMBL
        Q7A260_NOSS1 | Q7A260: 1j57 1ktu

(-) Related Entries Specified in the PDB File

1zm8 APO STRUCTURE OF NUCA