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(-) Description

Title :  MTH0212 IN COMPLEX WITH TWO DNA HELICES
 
Authors :  K. Lakomek, A. Dickmanns, R. Ficner
Date :  16 Feb 09  (Deposition) - 09 Mar 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,D,F,G,H
Biol. Unit 1:  A,D,F  (1x)
Biol. Unit 2:  B,G,H  (1x)
Keywords :  Protein-Dna Complex, Twin, Disorder Of Dna, 3'-5' Exonuclease, Ap Endonuclease, 2'-Desoxyuridine Endonuclease, 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(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3'
    Chains: F, H
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3'
    Chains: G, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABDFGH
Biological Unit 1 (1x): A DF  
Biological Unit 2 (1x):  B  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 24)

Asymmetric Unit (4, 24)
No.NameCountTypeFull Name
1DU2Mod. Residue
2GOL19Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 11)
No.NameCountTypeFull Name
1DU-1Mod. Residue
2GOL11Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1DU-1Mod. Residue
2GOL8Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:1088 , ALA A:1131 , GLU A:1134 , ARG B:2090 , HOH B:9027BINDING SITE FOR RESIDUE GOL A 7002
02AC2SOFTWAREMET A:1027 , GLU A:1054 , GLY A:1055 , LYS A:1076BINDING SITE FOR RESIDUE GOL A 7004
03AC3SOFTWARELEU A:1004 , ILE A:1033 , VAL A:1077 , PHE A:1102 , NA A:7401BINDING SITE FOR RESIDUE GOL A 7006
04AC4SOFTWARELYS A:1020 , ASP A:1242 , MET A:1244 , HOH A:9105BINDING SITE FOR RESIDUE GOL A 7010
05AC5SOFTWAREVAL A:1176 , ALA A:1179 , TRP A:1180 , LYS A:1183 , HOH A:9199 , HOH A:9219BINDING SITE FOR RESIDUE GOL A 7012
06AC6SOFTWAREHOH A:459 , LYS A:1183 , GLU A:1186 , ASN A:1187 , GLU B:2054 , HOH B:9172BINDING SITE FOR RESIDUE GOL A 7013
07AC7SOFTWAREPRO A:1043 , GLU A:1044 , LEU A:1046 , ARG A:1051 , GLU B:2228 , GLU B:2229 , HOH B:9174BINDING SITE FOR RESIDUE GOL A 7015
08AC8SOFTWAREGLY A:1055 , TYR A:1056 , ARG A:1057 , LYS A:1076 , ASP B:2182 , GLU B:2186BINDING SITE FOR RESIDUE GOL A 7020
09AC9SOFTWAREASP A:1103 , ASP A:1104BINDING SITE FOR RESIDUE GOL A 7024
10BC1SOFTWAREARG A:1090 , GLU A:1120 , LYS A:1123 , TYR A:1124 , GLU A:1127 , ARG B:2138BINDING SITE FOR RESIDUE GOL A 7030
11BC2SOFTWAREHOH A:443 , ILE A:1185 , TYR A:1189 , VAL A:1190 , ASP A:1191 , ARG A:1194 , HOH A:9268BINDING SITE FOR RESIDUE GOL A 7031
12BC3SOFTWAREASP A:1032 , THR A:1075 , LYS A:1076 , VAL A:1077 , GOL A:7006 , HOH A:9008BINDING SITE FOR RESIDUE NA A 7401
13BC4SOFTWAREGLU B:2094 , GLU B:2120 , ARG B:2121 , HOH B:9353BINDING SITE FOR RESIDUE GOL B 7003
14BC5SOFTWAREGLY A:1087 , VAL A:1088 , GLU A:1089 , GLY B:2087 , VAL B:2088 , GLU B:2089 , ASP B:2092 , HOH B:9144 , HOH B:9194BINDING SITE FOR RESIDUE GOL B 7011
15BC6SOFTWAREGLU B:2158 , ILE B:2159 , LEU B:2161 , PRO B:2164 , PRO B:2200 , HOH B:9118 , HOH B:9167 , HOH B:9306BINDING SITE FOR RESIDUE GOL B 7021
16BC7SOFTWAREASN B:2114 , LYS B:2116 , LYS B:2125 , ASN B:2153 , SER B:2171 , GLY B:2172 , LEU B:2221 , HOH B:9222BINDING SITE FOR RESIDUE GOL B 7022
17BC8SOFTWAREPRO B:2062 , GLU B:2084 , HOH B:9090 , HOH B:9109BINDING SITE FOR RESIDUE GOL B 7027
18BC9SOFTWARESER B:2168 , ASN B:2169 , PRO B:2175 , HOH B:9014BINDING SITE FOR RESIDUE GOL B 7032
19CC1SOFTWAREASP B:2191 , THR B:2192 , PHE B:2193 , ARG B:2220 , ASP B:2222 , TYR B:2223 , PHE B:2224 , TRP B:2238 , ILE B:2239 , ILE B:2251 , HOH B:9377BINDING SITE FOR RESIDUE GOL B 7033
20CC2SOFTWARELEU B:2082 , ARG B:2083BINDING SITE FOR RESIDUE PO4 B 7204
21CC3SOFTWAREASP B:2104 , LYS B:2233 , ILE B:2255 , GLU B:2256BINDING SITE FOR RESIDUE PO4 B 7205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GA6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GA6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GA6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GA6)

(-) Exons   (0, 0)

(no "Exon" information available for 3GA6)

(-) 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: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 d3ga6a_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh....eeeee.........eeeee......ee....hhhhhh...eeeee...eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhh............hhhhhhhhhhhhhh.eee.hhhh........ee...........ee..eeeeee..hhh.eeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ga6 A 1003 VLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGNFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIE 1256
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252    


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 d3ga6b_ 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.eeehhhhhh........................eeeeee.hhh....eeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ga6 B 2002 AVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGNFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIE 2256
                                  2011      2021      2031      2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211      2221      2231      2241      2251     


Chain D from PDB  Type:DNA  Length:12
                                             
                3ga6 D    1 GCCCTGxGCAGC   12
                                  | 10  
                                  7-DU  


Chain F from PDB  Type:DNA  Length:11
                                            
                3ga6 F    1 GCTGCGCAGGG   11
                                    10 


Chain G from PDB  Type:DNA  Length:12
                                             
                3ga6 G    1 GCCCTGxGCAGC   12
                                  | 10  
                                  7-DU  


Chain H from PDB  Type:DNA  Length:11
                                            
                3ga6 H    1 CTGCGCAGGGC   11
                                    10
   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 3GA6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GA6)

(-) 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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  3ga6
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  O26314_METTH | O26314
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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 3g4t 3g8v 3g91 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
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