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(-) Description

Title :  COMPLEX OF MTH0212 AND A 4 BP DSDNA WITH 3'-OVERHANG
 
Authors :  K. Lakomek, A. Dickmanns, R. Ficner
Date :  31 Jan 09  (Deposition) - 09 Mar 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,G,H,I,K
Biol. Unit 1:  A,G,K  (1x)
Biol. Unit 2:  B,H,I  (1x)
Keywords :  Protein-Dna Complex, Dsdna With 3'-Overhang, 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 (D151N)
    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*CP*G*CP*AP*GP*GP*C)-3'
    Chains: G, H
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3'
    Chains: K, I
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABGHIK
Biological Unit 1 (1x): A G  K
Biological Unit 2 (1x):  B HI 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1DU2Mod. Residue
2GOL7Ligand/IonGLYCEROL
3PG44Ligand/IonTETRAETHYLENE GLYCOL
4PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1DU-1Mod. Residue
2GOL6Ligand/IonGLYCEROL
3PG43Ligand/IonTETRAETHYLENE GLYCOL
4PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DU-1Mod. Residue
2GOL1Ligand/IonGLYCEROL
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:209 , THR A:210 , HOH A:315 , HOH A:407 , DC K:1BINDING SITE FOR RESIDUE PO4 A 266
02AC2SOFTWAREGLU A:228 , GLU A:229 , LYS A:231 , GLY A:232 , HOH A:325BINDING SITE FOR RESIDUE PO4 A 267
03AC3SOFTWARELYS A:116 , ASN A:169 , VAL A:170 , SER A:171 , HOH A:390 , ASN B:169BINDING SITE FOR RESIDUE PO4 A 268
04AC4SOFTWAREASN A:12 , ASN A:114 , GLY A:115 , LYS A:116 , LYS A:125 , ASN A:153 , SER A:171 , GLY A:172 , GLU A:177 , TRP A:205 , LEU A:221 , ASP A:247 , HOH A:277 , DG G:7BINDING SITE FOR RESIDUE PG4 A 269
05AC5SOFTWARETRP A:206 , SER A:207 , TYR A:208 , ARG A:211 , ARG A:213 , MET A:244 , SER A:246 , ASP A:247 , GOL A:274 , DC K:1 , DC K:2BINDING SITE FOR RESIDUE PG4 A 270
06AC6SOFTWAREHIS A:156 , ARG A:157 , ILE A:185 , ASP A:191 , HOH A:355BINDING SITE FOR RESIDUE GOL A 271
07AC7SOFTWAREARG A:51 , HIS A:52 , VAL A:53 , TYR A:56BINDING SITE FOR RESIDUE PG4 A 272
08AC8SOFTWAREGLU A:89 , ARG A:90 , THR A:93BINDING SITE FOR RESIDUE GOL A 273
09AC9SOFTWARELYS A:20 , TYR A:208 , MET A:244 , GLY A:245 , SER A:246 , PG4 A:270 , HOH A:312BINDING SITE FOR RESIDUE GOL A 274
10BC1SOFTWAREARG A:213 , SER A:241 , ASP A:242 , HOH A:297BINDING SITE FOR RESIDUE GOL A 275
11BC2SOFTWARELYS B:183 , GLU B:186 , ASN B:187 , HOH B:281BINDING SITE FOR RESIDUE PG4 B 266
12BC3SOFTWAREARG B:48 , ARG B:51BINDING SITE FOR RESIDUE GOL B 267
13BC4SOFTWAREHOH K:83BINDING SITE FOR RESIDUE GOL K 11

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G2D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G2D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G2D)

(-) Exons   (0, 0)

(no "Exon" information available for 3G2D)

(-) 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:256
 aligned with O26314_METTH | O26314 from UniProtKB/TrEMBL  Length:257

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
         O26314_METTH     2 TVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIEL 257
               SCOP domains d3g2da_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhh.hhhhhhhhhh..eeeee....hhhhhhhhhhh....eeeee.........eeeee.....eee....hhhhhh...eeeee....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh..hhhhh.....hhhhhhhhhhhhhh.eee.hhhh...........hhhhhhhhh.....eeeeee.hhhh.eeeeee...........eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g2d A   2 AVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGNFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIEL 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      


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

    Alignment length:255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         O26314_METTH     2 TVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIE 256
               SCOP domains d3g2db_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhh.hhhhhhhhhh..eeeee....hhhhhhhhhhh....eeeee.........eeeee.....eee....hhhhhh...eeeee....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh..hhhhh.....hhhhhhhhhhhhhh.eee.hhhh...........hhhhhhhhh.....eeeeee.hhhh.eeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g2d B   2 AVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGNFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIE 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     


Chain G from PDB  Type:DNA  Length:4
                                    
                 3g2d G   4 CAGG   7


Chain H from PDB  Type:DNA  Length:4
                                    
                 3g2d H   4 CAGG   7


Chain I from PDB  Type:DNA  Length:9
                                         
                 3g2d I   1 CCTGxGCGA   9
                                |    
                                5-DU 


Chain K from PDB  Type:DNA  Length:8
                                        
                 3g2d K   1 CCTGxGCG   8
                                |   
                                5-DU
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G2D)

(-) Gene Ontology  (7, 7)

Asymmetric 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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  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 3g38 3g3c 3g3y 3g4t 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)
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
3g4t MTH0212 (WT) IN COMPLEX WITH A 7BP DSDNA
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