Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH AN ORPHAN ADENINE BASE
 
Authors :  D. Lu, J. Silhan, J. T. Macdonald, E. P. Carpenter, K. Jensen, C. M. Tang, G. S. Baldwin, P. S. Freemont
Date :  03 Aug 12  (Deposition) - 17 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,U,V
Keywords :  Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Lu, J. Silhan, J. T. Macdonald, E. P. Carpenter, K. Jensen, C. M. Tang G. S. Baldwin, P. S. Freemont
Structural Basis For The Recognition And Cleavage Of Abasic Dna In Neisseria Meningitidis.
Proc. Natl. Acad. Sci. Usa V. 109 16852 2012
PubMed-ID: 23035246  |  Reference-DOI: 10.1073/PNAS.1206563109

(-) Compounds

Molecule 1 - PUTATIVE EXODEOXYRIBONUCLEASE
    Chains: A
    EC Number: 3.1.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 487
    Synonym: NEISSERIA AP ENDONUCLEASE
 
Molecule 2 - 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
    Chains: U
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 487
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*AP*TP*GP*AP*GP*TP*AP*GP*CP)-3'
    Chains: V
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 487
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AUV

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4B5J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B5J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B5J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B5J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B5J)

(-) Exons   (0, 0)

(no "Exon" information available for 4B5J)

(-) 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:256
 aligned with Q7DD47_NEIMB | Q7DD47 from UniProtKB/TrEMBL  Length:259

    Alignment length:256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      
         Q7DD47_NEIMB     1 MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLVVEYDY 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhheeeee.........eeeee.....eeee...hhhhhh...eeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhh.............hhhhhhhhhhhhhh...eehhhhhh.............hhhhhh.....eeeeehhhhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5j A   1 MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLVVEYDY 256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      


Chain U from PDB  Type:DNA  Length:11
                                           
                 4b5j U  31 GCTACxCATCG  41
                                 |  40 
                                36-3DR 


Chain V from PDB  Type:DNA  Length:11
                                           
                 4b5j V  42 CGATGAGTAGC  52
                                    51
   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 4B5J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B5J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B5J)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7DD47_NEIMB | Q7DD47)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0008853    exodeoxyribonuclease III activity    Catalysis of the degradation of double-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides.
    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.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    3DR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4b5j)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4b5j)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4b5j
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q7DD47_NEIMB | Q7DD47
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.1.11.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q7DD47_NEIMB | Q7DD47
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7DD47_NEIMB | Q7DD47: 2jc5 4b5f 4b5g 4b5h 4b5i 4b5m

(-) Related Entries Specified in the PDB File

4b5f SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS (CRYSTAL FORM 1)
4b5g SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS (CRYSTAL FORM 2)
4b5h SUBSTATE BOUND INACTIVE MUTANT OF NEISSERIA AP ENDONUCLEASE IN PRESENCE OF METAL IONS
4b5i PRODUCT COMPLEX OF NEISSERIA AP ENDONUCLEASE IN PRESENCE OF METAL IONS
4b5m NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH A CYTOSINE ORPHAN BASE