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(-) Description

Title :  CRYSTAL STRUCTURE OF TM1865, AN ENDONUCLEASE V FROM THERMOTOGA MARITIMA
 
Authors :  D. Utepbergenov, D. R. Cooper, U. Derewenda, Z. S. Derewenda, Integrated Center For Structure And Function Innovation (Isfi)
Date :  06 May 09  (Deposition) - 14 Jul 09  (Release) - 14 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  D  (1x)
Keywords :  Structural Genomics, Isfi, Rnaseh Superfamily, Endonuclease V, Psi-2, Protein Structure Initiative, Integrated Center For Structure And Function Innovation, Cytoplasm, Dna Damage, Dna Repair, Endonuclease, Hydrolase, Magnesium, Nuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Utepbergenov, D. R. Cooper, U. Derewenda, Z. S. Derewenda
Crystal Structure Of Tm1865, An Endonuclease V From Thermotoga Maritima
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDONUCLEASE V
    Chains: A, B, D
    EC Number: 3.1.21.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: NFI, TM_1865
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: DEOXYINOSINE 3'ENDONUCLEASE, DEOXYRIBONUCLEASE V, DNASE V

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABD
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3HD0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HD0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:61 -Pro A:62
2Pro A:202 -Gly A:203
3Tyr B:61 -Pro B:62
4Tyr D:61 -Pro D:62

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HD0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HD0)

(-) Exons   (0, 0)

(no "Exon" information available for 3HD0)

(-) 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:220
 aligned with NFI_THEMA | Q9X2H9 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
            NFI_THEMA     1 MDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRL 220
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh............eeeeeeee.....eeeeeeeeee....eeeeeeeeeee.........hhhhhhhhhhhhhh.......eeeee..........hhhhhhhhhhh..eeeee.................eeeeee..eeeeeee........eeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd0 A   1 mDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHmGLFIEIPTIGVAKSRLYGTFKmPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLmDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRL 220
                            |       10        20        30        40        50        60        70        80        90       100       110       120     | 130       140       150       160       170       180      |190       200       210       220
                            |                                                                                                                          126-MSE               148-MSE                                187-MSE                             
                            1-MSE                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:216
 aligned with NFI_THEMA | Q9X2H9 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:216
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215      
            NFI_THEMA     6 LHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLK 221
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh............eeeeeeeeeee..eeeeeeeeee.....eeeeeeeeee.........hhhhhhhhhhhhhhh......eeeee..........hhhhhhhhhhh..eeeee......ee.........eeeeee..eeeeeee........eeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hd0 B   6 LHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHmGLFIEIPTIGVAKSRLYGTFKmPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLmDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLK 221
                                    15        25        35        45        55        65        75        85        95       105       115       125|      135       145  |    155       165       175       185 |     195       205       215      
                                                                                                                                                  126-MSE               148-MSE                                187-MSE                              


Chain D from PDB  Type:PROTEIN  Length:223
 aligned with NFI_THEMA | Q9X2H9 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:223
                              1                                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
            NFI_THEMA     - --MDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLK 221
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhh..........eeeeeeeeeee..eeeeeeeeee.....eeeeeeeeee.........hhhhhhhhhhhhhh.......eeeee..........hhhhhhhhhhh..eeeee.................eeeeee..eeeeeee........eeeee....hhhhhhhhhhhh.......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd0 D  -1 HHmDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHmGLFIEIPTIGVAKSRLYGTFKmPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLmDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLK 221
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
                              1-MSE                                                                                                                      126-MSE               148-MSE                                187-MSE
   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 3HD0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HD0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HD0)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D   (NFI_THEMA | Q9X2H9)
molecular function
    GO:0043737    deoxyribonuclease V activity    Catalysis of the endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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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 Related Entries

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        NFI_THEMA | Q9X2H9: 2w35 2w36 4b20

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