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(-) Description

Title :  XPF FROM AEROPYRUM PERNIX
 
Authors :  M. Newman, J. Murray-Rust, J. Lally, J. Rudolf, A. Fadden, P. P. Knowles, M. F. White, N. Q. Mcdonald
Date :  14 Jan 05  (Deposition) - 23 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Hydrolase, Structure Specific Endonuclease, Nucleotide Excision Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Newman, J. Murray-Rust, J. Lally, J. Rudolf, A. Fadden, P. P. Knowles, M. F. White, N. Q. Mcdonald
Structure Of An Xpf Endonuclease With And Without Dna Suggests A Model For Substrate Recognition
Embo J. V. 24 895 2005
PubMed-ID: 15719018  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600581

(-) Compounds

Molecule 1 - XPF ENDONUCLEASE
    Chains: A, B, C, D
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-14B-3C
    Expression System Strain: ROSETTA/PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: 19-231
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Other Details: A PERNIX GENOME SEQUENCING PROJECT GNE APE 1436, ACCESSION CODE C72622

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): AB  
Biological Unit 2 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2BHN)

(-) Sites  (0, 0)

(no "Site" information available for 2BHN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BHN)

(-) Exons   (0, 0)

(no "Exon" information available for 2BHN)

(-) 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:211
 aligned with Q9YC15_AERPE | Q9YC15 from UniProtKB/TrEMBL  Length:248

    Alignment length:211
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
         Q9YC15_AERPE    13 PRVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTREGGQRIVIHKKPRLSDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 223
               SCOP domains d2bhna2 A:19-148 XPF endonuclease                                                                                                 -----------d2bhna1 A:160-229 DNA repair endonuclease XPF                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhh...eeeee......eeee..eeeeeeehhhhhhhhhh.hhhhhhhhhhh...eeeeeee....hhhhh.hhhhhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhh................hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bhn A  19 PRVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTREGGQRIVIHKKPRLSDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 229
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228 


Chain B from PDB  Type:PROTEIN  Length:199
 aligned with Q9YC15_AERPE | Q9YC15 from UniProtKB/TrEMBL  Length:248

    Alignment length:211
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
         Q9YC15_AERPE    13 PRVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTREGGQRIVIHKKPRLSDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 223
               SCOP domains d2bhnb2 B:19-148 XPF endonuclease                                                                                                 -------------d2bhnb1 B:162-229 DNA repair endonuclease XPF                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhh.hhhhhhhh...eeeee......ee....eeeeeeehhhhhhhhh..hhhhhhhhhhhhh.eeeeeee....hhhhh.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhh.------------..hhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhh.hhhhhh.....hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bhn B  19 PRVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTR------------RLSDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 229
                                    28        38        48        58        68        78        88        98       108       118       128       138       148|        -   |   168       178       188       198       208       218       228 
                                                                                                                                                            149          162                                                                   


Chain C from PDB  Type:PROTEIN  Length:194
 aligned with Q9YC15_AERPE | Q9YC15 from UniProtKB/TrEMBL  Length:248

    Alignment length:210
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
         Q9YC15_AERPE    14 RVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTREGGQRIVIHKKPRLSDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 223
               SCOP domains d2bhnc2 C:20-147 XPF endonuclease                                                                                               ----------------d2bhnc1 C:164-229 DNA repair endonuclease XPF                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.hhh...hhhhhh.....eeee......eeee..eeeeeeehhhhhhhhh..hhhhhhhhhhh...eeeeeee....hhhhh.hhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh.----------------hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bhn C  20 RVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLS----------------SDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 229
                                    29        39        49        59        69        79        89        99       109       119       129       139       | -         -    |  169       179       189       199       209       219       229
                                                                                                                                                         147              164                                                                 


Chain D from PDB  Type:PROTEIN  Length:211
 aligned with Q9YC15_AERPE | Q9YC15 from UniProtKB/TrEMBL  Length:248

    Alignment length:211
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
         Q9YC15_AERPE    13 PRVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTREGGQRIVIHKKPRLSDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 223
               SCOP domains d2bhnd2 D:19-148 XPF endonuclease                                                                                                 -----------d2bhnd1 D:160-229 DNA repair endonuclease XPF                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhh..eeeee......ee....eeeeeeehhhhhhhhh..hhhhhhhhhhhhh.eeeeeee....hhhhh.hhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh..................hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bhn D  19 PRVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTREGGQRIVIHKKPRLSDVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 229
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228
   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, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BHN)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9YC15_AERPE | Q9YC15)
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: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.
biological process
    GO:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    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.

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  2bhn
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 Related Entries

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

UniProtKB/TrEMBL
        Q9YC15_AERPE | Q9YC15: 2bgw

(-) Related Entries Specified in the PDB File

2bgw XPF FROM AEROPYRUM PERNIX, COMPLEX WITH DNA