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(-) Description

Title :  MTH0212 (WT) IN COMPLEX WITH A 7BP DSDNA
 
Authors :  K. Lakomek, A. Dickmanns, R. Ficner
Date :  04 Feb 09  (Deposition) - 09 Mar 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym./Biol. Unit :  A,B,H,I
Keywords :  Protein-Dna Complex, Double-Stranded Dna, Inorganic Phosphate, Mg2+, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Lakomek, A. Dickmanns, E. Ciirdaeva, L. Schomacher, R. Ficner
Crystal Structure Analysis Of Dna Uridine Endonuclease Mth212 Bound To Dna
J. Mol. Biol. V. 399 604 2010
PubMed-ID: 20434457  |  Reference-DOI: 10.1016/J.JMB.2010.04.044
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXODEOXYRIBONUCLEASE
    Chains: A, B
    EC Number: 3.1.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET_B_001-MTH212 (WT)
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MTH0212, MTH212, MTH_212
    Mutation: YES
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 187420
    Strain: DELTA H (DSM 1053)
    Synonym: MTH0212
 
Molecule 2 - 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3'
    Chains: H
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*G*TP*AP*CP*TP*AP*CP*G)-3'
    Chains: I
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PO43Ligand/IonPHOSPHATE ION
3UPS1Mod. Nucleotide2'-DEOXY-5'-O-THIOPHOSPHONOURIDINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:10 , GLU A:38 , TYR A:111 , ASN A:114 , ASP A:151 , ASN A:153 , HIS A:248 , MG A:267 , DA H:7BINDING SITE FOR RESIDUE PO4 A 266
2AC2SOFTWAREASN A:10 , ASN A:12 , GLU A:38 , ASP A:247 , HIS A:248 , PO4 A:266 , DA H:7BINDING SITE FOR RESIDUE MG A 267
3AC3SOFTWAREASN B:10 , GLU B:38 , TYR B:111 , ASN B:114 , ASP B:151 , ASN B:153 , HIS B:248 , MG B:267 , DG I:9BINDING SITE FOR RESIDUE PO4 B 266
4AC4SOFTWAREASN B:10 , GLU B:38 , ASP B:247 , HIS B:248 , PO4 B:266 , DG I:9BINDING SITE FOR RESIDUE MG B 267
5AC5SOFTWAREARG A:209 , ARG A:211 , DC H:1 , DT I:3BINDING SITE FOR RESIDUE PO4 I 10

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G4T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G4T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G4T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G4T)

(-) Exons   (0, 0)

(no "Exon" information available for 3G4T)

(-) 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:254
 aligned with O26314_METTH | O26314 from UniProtKB/TrEMBL  Length:257

    Alignment length:254
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    
         O26314_METTH     3 VLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIE 256
               SCOP domains d3g4ta_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeeee.........eeeee......ee....hhhhhh...eeeee...eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhh............hhhhhhhhhhhhhh.eeehhhhhh.............hhhhhh.....eeeeee.hhhh.eeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4t A   3 VLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIE 256
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with O26314_METTH | O26314 from UniProtKB/TrEMBL  Length:257

    Alignment length:255
                                    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     
         O26314_METTH     1 MTVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEI 255
               SCOP domains d3g4tb_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhh.hhhhhhhhh...eeeee....hhhhhhhhhhh....eeeee.........eeeee......ee....hhhhhh...eeeee...eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhh............hhhhhhhhhhhhhh.eeehhhhhh.............hhhhhh.....eeeeee.hhhhhh.eeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4t B   1 MAVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEI 255
                                    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 H from PDB  Type:DNA  Length:7
                                       
                 3g4t H   1 CGTAxTA   7
                                |  
                                5-UPS


Chain I from PDB  Type:DNA  Length:7
                                       
                 3g4t I   3 TACTACG   9
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G4T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G4T)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O26314_METTH | O26314)
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: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.

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  3g4t
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  O26314_METTH | O26314
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  3.1.11.2
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 Related Entries

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

UniProtKB/TrEMBL
        O26314_METTH | O26314: 3fzi 3g00 3g0a 3g0r 3g1k 3g2c 3g2d 3g38 3g3c 3g3y 3g8v 3g91 3ga6 3w2x 3w2y

(-) Related Entries Specified in the PDB File

3fzi 1.9 ANGSTROM STRUCTURE OF THE THERMOPHILIC EXONUCLEASE III HOMOLOGUE MTH0212
3g00 MTH0212 IN COMPLEX WITH A 9BP BLUNT END DSDNA AT 1.7 ANGSTROM
3g0a MTH0212 WITH TWO BOUND MANGANESE IONS
3g0r COMPLEX OF MTH0212 AND AN 8BP DSDNA WITH DISTORTED ENDS
3g1k MTH0212 (WT) CRYSTALLIZED IN A MONOCLINIC SPACE GROUP
3g2c MTH0212 IN COMPLEX WITH A SHORT SSDNA (CGTA)
3g2d COMPLEX OF MTH0212 AND A 4 BP DSDNA WITH 3'-OVERHANG
3g38 THE CATALYTICALLY INACTIVE MUTANT MTH0212 (D151N) IN COMPLEX WITH AN 8 BP DSDNA
3g3c MTH0212 (WT) IN COMPLEX WITH A 6BP DSDNA CONTAINING A SINGLE ONE NUCLEOTIDE LONG 3'-OVERHANG
3g3y MTH0212 IN COMPLEX WITH SSDNA IN SPACE GROUP P32
3g8v THE RATIONALLY DESIGNED CATALYTICALLY INACTIVE MUTANT MTH0212(D151N)
3g91 1.2 ANGSTROM STRUCTURE OF THE EXONUCLEASE III HOMOLOGUE MTH0212
3ga6 MTH0212 IN COMPLEX WITH TWO DNA HELICES