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(-) Description

Title :  CRYSTAL STRUCTURE OF TOPOISOMERASE V FROM METHANOPYRUS KANDLERI (61 KDA FRAGMENT)
 
Authors :  B. Taneja, A. Patel, A. Slesarev, A. Mondragon
Date :  21 May 05  (Deposition) - 31 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Topoisomerase Ib, Topoisomerase V, Helix-Turn-Helix, Helix-Hairpin- Helix, Hhh Motif, Three Helix Bundle, Methanopyrus Kandleri, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Taneja, A. Patel, A. Slesarev, A. Mondragon
Structure Of The N-Terminal Fragment Of Topoisomerase V Reveals A New Family Of Topoisomerases
Embo J. V. 25 398 2006
PubMed-ID: 16395333  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600922

(-) Compounds

Molecule 1 - TOPOISOMERASE V
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET14B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERM 61 KDA FRAGMENT
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 2320
    Synonym: TOP61

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:3053 , HOH A:3054 , HOH A:3055 , HOH A:3056 , HOH A:3057 , HOH A:3058 , HOH A:3302BINDING SITE FOR RESIDUE MG A 3052

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:314 -A:338
2B:314 -B:338

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CSB)

(-) 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:517
 aligned with Q977W1_9EURY | Q977W1 from UniProtKB/TrEMBL  Length:984

    Alignment length:517
                                    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       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       
         Q977W1_9EURY     3 LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKLQDRYGIREDVALCLARAFDGSISMIATTPYRTLKDVCPDLTLEEAKSVNRTLATLIDEHGLSPDAADELIEHFESIAGILATDLEEIERMYEEGRLSEEAYRAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEELREDGLTDAQIRELKGLK 519
               SCOP domains d2csba5 A:3-293 Topoisomerase V, catalytic domain                                                                                                                                                                                                                                                  d2csba2 A:294-350 Topoisomerase V                        d2csba1 A:351-409 Topoisomerase V                          d2csba3 A:410-464 Topoisomerase V                      d2csba4 A:465-519 Topoisomerase V                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee..eehhhhhhh.....hhhhhhhh...hhhhhhhhh..hhhhh.............hhhhhhhhhhh........hhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2csb A   3 LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLmERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLmPVTVDEVPPEmAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDImRRYLEQRIVECALKLQDRYGIREDVALCLARAFDGSISmIATTPYRTLKDVCPDLTLEEAKSVNRTLATLIDEHGLSPDAADELIEHFESIAGILATDLEEIERmYEEGRLSEEAYRAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEELREDGLTDAQIRELKGLK 519
                                    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       262       272       282   |   292       302       312       322  |    332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       
                                                                40-MSE                                                                                                            155-MSE    166-MSE                                                                                                                 286-MSE                                325-MSE                                                           391-MSE                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:517
 aligned with Q977W1_9EURY | Q977W1 from UniProtKB/TrEMBL  Length:984

    Alignment length:517
                                    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       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       
         Q977W1_9EURY     3 LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKLQDRYGIREDVALCLARAFDGSISMIATTPYRTLKDVCPDLTLEEAKSVNRTLATLIDEHGLSPDAADELIEHFESIAGILATDLEEIERMYEEGRLSEEAYRAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEELREDGLTDAQIRELKGLK 519
               SCOP domains d2csbb1 B:3-293 Topoisomerase V, catalytic domain                                                                                                                                                                                                                                                  d2csbb2 B:294-350 Topoisomerase V                        d2csbb3 B:351-409 Topoisomerase V                          d2csbb4 B:410-464 Topoisomerase V                      d2csbb5 B:465-519 Topoisomerase V                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee..eehhhhhhhh....hhhhhhhh...hhhhhhhhh..hhhhh.............hhhhhhhhhhh........hhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhh.hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2csb B   3 LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLmERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLmPVTVDEVPPEmAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDImRRYLEQRIVECALKLQDRYGIREDVALCLARAFDGSISmIATTPYRTLKDVCPDLTLEEAKSVNRTLATLIDEHGLSPDAADELIEHFESIAGILATDLEEIERmYEEGRLSEEAYRAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEELREDGLTDAQIRELKGLK 519
                                    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       262       272       282   |   292       302       312       322  |    332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       
                                                                40-MSE                                                                                                            155-MSE    166-MSE                                                                                                                 286-MSE                                325-MSE                                                           391-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  (2, 10)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q977W1_9EURY | Q977W1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
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.

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 Related Entries

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        Q977W1_9EURY | Q977W1: 2csd 3m6k 3m6z 3m7d 3m7g 5hm5

(-) Related Entries Specified in the PDB File

2csd