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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF A REPAIR ENDONUCLEASE FROM PYROCOCCUS ABYSSI
 
Authors :  B. Ren, J. Kuhn, L. Meslet-Cladiere, J. Briffotaux, C. Norais, R. Lavig D. Flament, R. Ladenstein, H. Myllykallio
Date :  14 Jan 08  (Deposition) - 19 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Endonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Ren, J. Kuhn, L. Meslet-Cladiere, J. Briffotaux, C. Norais, R. Lavigne, D. Flament, R. Ladenstein, H. Myllykallio
Structure And Function Of A Novel Endonuclease Acting On Branched Dna Substrates.
Embo J. V. 28 2479 2009
PubMed-ID: 19609302  |  Reference-DOI: 10.1038/EMBOJ.2009.192

(-) Compounds

Molecule 1 - UPF0286 PROTEIN PYRAB01260
    Chains: A, B
    Mutation: YES
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Synonym: NUCS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2VLD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VLD)

(-) 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:228
 aligned with NUCS_PYRAB | Q9V2E8 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
           NUCS_PYRAB     1 MRKVIIKENPSEEEIKELLDLAEKHGGVVTIFARCKVHYEGRAKSELGEGDRIIIIKPDGSFLIHQNKKREPVNWQPPGSKVTFKENSIISIRRRPYERLEVEIIEPYSLVVFLAEDYEELALTGSEAEMANLIFENPRVIEEGFKPIYREKPIRHGIVDVMGVDKDGNIVVLELKRRKADLHAVSQLKRYVDSLKEEYGENVRGILVAPSLTEGAKKLLEKEGLEFRKLEPP 233
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhhhhhhhhhhhh.eeeeeeeeeeeee...eeeeeeeeeeeee.....eeee........eee....eeee..eeeeee.....eeeeeeeeeeeeeeee.......-----hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhh.eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vld A   1 mRKVIIKENPSEEEIKELLDLAEKHGGVVTIFARCKVHYEGRAKSELGEGDRIIIIKPDGSFLIHQNKKREPVNWQPPGSKVTFKENSmISIRRRPYERLEVEIIEPYSLVVFLAEDYEE-----SEAEmANLIFENPRVIEEGFKPIYREKPIRHGIVDVmGVDKDGNIVVLELKRRKADLHAVSQmKRYVDSLKEEYGENVRGILVAPSLTEGAKKLLEKEGLEFRKLEPP 233
                            |       10        20        30        40        50        60        70        80        90       100       110       120     | 130       140       150       160 |     170       180       190       200       210       220       230   
                            |                                                                                      89-MSE                        120   126   |                             162-MSE                   188-MSE                                         
                            1-MSE                                                                                                                          130-MSE                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with NUCS_PYRAB | Q9V2E8 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:231
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
           NUCS_PYRAB     3 KVIIKENPSEEEIKELLDLAEKHGGVVTIFARCKVHYEGRAKSELGEGDRIIIIKPDGSFLIHQNKKREPVNWQPPGSKVTFKENSIISIRRRPYERLEVEIIEPYSLVVFLAEDYEELALTGSEAEMANLIFENPRVIEEGFKPIYREKPIRHGIVDVMGVDKDGNIVVLELKRRKADLHAVSQLKRYVDSLKEEYGENVRGILVAPSLTEGAKKLLEKEGLEFRKLEPP 233
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhhhhh.eeeeeeeeeeeee...eeeeeeeeeeeee.....eeee........eee....eeee..eeeeee.....eeeeeeeeeeeeeeee.......-----hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhh.eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vld B   3 KVIIKENPSEEEIKELLDLAEKHGGVVTIFARCKVHYEGRAKSELGEGDRIIIIKPDGSFLIHQNKKREPVNWQPPGSKVTFKENSmISIRRRPYERLEVEIIEPYSLVVFLAEDYEE-----SEAEmANLIFENPRVIEEGFKPIYREKPIRHGIVDVmGVDKDGNIVVLELKRRKADLHAVSQmKRYVDSLKEEYGENVRGILVAPSLTEGAKKLLEKEGLEFRKLEPP 233
                                    12        22        32        42        52        62        72        82      | 92       102       112       | -   |   132       142       152       162       172       182     | 192       202       212       222       232 
                                                                                                                 89-MSE                        120   126   |                             162-MSE                   188-MSE                                         
                                                                                                                                                         130-MSE
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 2VLD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NUCS_PYRAB | Q9V2E8)
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: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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0000014    single-stranded DNA endodeoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.
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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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