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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE YEAST TYROSYL-DNA PHOSPHODIESTERASE 1 H432R MUTANT (SCAN1 MUTANT)
 
Authors :  S. Gajewski, S. W. White
Date :  05 Jul 11  (Deposition) - 28 Dec 11  (Release) - 14 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),C (1x)
Biol. Unit 6:  B,D  (1x)
Keywords :  Phosphodiesterase, Dna Binding, Nuclear, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Gajewski, E. Q. Comeaux, N. Jafari, N. Bharatham, D. Bashford, S. W. White, R. C. Van Waardenburg
Analysis Of The Active-Site Mechanism Of Tyrosyl-Dna Phosphodiesterase I: A Member Of The Phospholipase D Superfamily.
J. Mol. Biol. V. 415 741 2012
PubMed-ID: 22155078  |  Reference-DOI: 10.1016/J.JMB.2011.11.044

(-) Compounds

Molecule 1 - TYROSYL-DNA PHOSPHODIESTERASE 1
    Chains: A, B, C, D
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 79-539
    Gene: TDP1, YBR223C, YBR1520
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: TYR-DNA PHOSPHODIESTERASE 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x) C (1x) 
Biological Unit 6 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NEP4Mod. Amino AcidN1-PHOSPHONOHISTIDINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NEP1Mod. Amino AcidN1-PHOSPHONOHISTIDINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NEP1Mod. Amino AcidN1-PHOSPHONOHISTIDINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NEP1Mod. Amino AcidN1-PHOSPHONOHISTIDINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1NEP1Mod. Amino AcidN1-PHOSPHONOHISTIDINE
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1NEP1Mod. Amino AcidN1-PHOSPHONOHISTIDINE
Biological Unit 6 (1, 2)
No.NameCountTypeFull Name
1NEP2Mod. Amino AcidN1-PHOSPHONOHISTIDINE

(-) Sites  (0, 0)

(no "Site" information available for 3SQ8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SQ8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:523 -Pro A:524
2Leu B:523 -Pro B:524
3Leu C:523 -Pro C:524
4Leu D:523 -Pro D:524

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SQ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SQ8)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR223C1YBR223C.1II:670292-6686581635TYDP1_YEAST1-5445444A:79-539 (gaps)
B:79-541 (gaps)
C:79-541 (gaps)
D:79-542 (gaps)		461
463
463
464

(-) 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:422
 aligned with TYDP1_YEAST | P38319 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:461
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538 
          TYDP1_YEAST    79 GAVFKLMKSDFYEREDFMGEVEDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSAGTSASDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPAKDTAGRKKAEILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATNSAGPCDASQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDRRGCAGNPTHVAVPFTLPVIPYDLAEDECFCLA 539
               SCOP domains d3sq8a1 A:79-29       3 automated matches                                                                                                                                                                              d      3sq8a2 A:294-539 automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........-------.eehhhhhhh...eeeeeee...eehhhhhh.......eeeeeee...ee.......hhhhhhhhh.eeeeee...........eeeeee...eeeeeee....hhhhhhh...eeee...eee......hhhhhhhhhhhhh..hhhhhhhhhhhhhheehhhhh..eeeee.......hhhhhhhhhhhhhh------..eeeeeee..............hhhhhhhhhhhhh.....-----------..hhhhhhhhhhhhheeeeee...hhhhhh..hhhhhhhhh......hhhhhhhhhhh...eee.................eeeeeeee--------.....ee.eeeee....hhhhhh.........eeeeeee.hhh.....eeeee....-------...eee......ee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:79-539 (gaps) UniProt: 1-544 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 3sq8 A  79 GAVFKLMKSDFYERE-------DMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHhTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLS------DTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPP-----------ILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPARSKFYMHCAT--------SQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRD-------PTHVAVPFTLPVIPYDLAEDECFCLA 539
                                    88    |    -  |    108       118       128       138       148       158       168       178   |   188       198       208       218       228       238       248       258       268       278       288     |   -  |    308       318       328       338  |      -    |  358       368       378       388       398       408       418       428       438  |      - |     458       468       478       488       498       | -     | 518       528       538 
                                         93     101                                                                              182-NEP                                                                                                         294    301                                     341         353                                                                                     441      450                                                     506     514                         


Chain B from PDB  Type:PROTEIN  Length:423
 aligned with TYDP1_YEAST | P38319 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:463
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538   
          TYDP1_YEAST    79 GAVFKLMKSDFYEREDFMGEVEDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSAGTSASDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPAKDTAGRKKAEILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATNSAGPCDASQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDRRGCAGNPTHVAVPFTLPVIPYDLAEDECFCLARH 541
               SCOP domains d3sq8b1 B:79-29       3 automated matches                                                                                                                                                                              d      3sq8b2 B:294-541 automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........-------.eehhhhhhh...eeeeeee...eehhhhhh.......eeeeeee...ee..hhhhhhhhhhhhhh.eeeeee...........eeeeee...eeeeeee....hhhhhhh...eeee...eee......hhhhhhhhhhhhh..hhhhhhhhhhhhhheehhhhh..eeeee.......hhhhhhhhhhhhhh------..eeeeeee..............hhhhhhhhhhhh......-----------..hhhhhhhhhhhhheeeeee...hhhhhh..hhhhhhhhh......hhhhhhhhhhh...eee.................eeeeeeee.-------.....ee.eeeee....hhhhhh.........eeeeeee.hhh.--..eeeee.hhh-------...eee......ee.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:79-541 (gaps) UniProt: 1-544 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                      Transcript 1
                 3sq8 B  79 GAVFKLMKSDFYERE-------DMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHhTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLS------DTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPP-----------ILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPARSKFYMHCATN-------SQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLA--RKVTCRTFTRD-------PTHVAVPFTLPVIPYDLAEDECFCLALH 541
                                    88    |    -  |    108       118       128       138       148       158       168       178   |   188       198       208       218       228       238       248       258       268       278       288     |   -  |    308       318       328       338  |      -    |  358       368       378       388       398       408       418       428       438   |     - |     458       468       478       488    |  498       | -     | 518       528       538   
                                         93     101                                                                              182-NEP                                                                                                         294    301                                     341         353                                                                                      442     450                                        493  |       506     514                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                           496                                             


Chain C from PDB  Type:PROTEIN  Length:423
 aligned with TYDP1_YEAST | P38319 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:463
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538   
          TYDP1_YEAST    79 GAVFKLMKSDFYEREDFMGEVEDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSAGTSASDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPAKDTAGRKKAEILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATNSAGPCDASQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDRRGCAGNPTHVAVPFTLPVIPYDLAEDECFCLARH 541
               SCOP domains d3sq8c1 C:79-29       3 automated matches                                                                                                                                                                              d      3sq8c2 C:294-541 automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........-------.eehhhhhhh...eeeeeee...eehhhhhh.......eeeeeee...ee..hhhhhhhhhhhhhh.eeeeee...........eeeeee...eeeeeee....hhhhhhh...eeee...eee......hhhhhhhhhhhhh..hhhhhhhhhhhhhheehhhhh..eeeee.......hhhhhhhhhhhhhh------..eeeeeee..............hhhhhhhhhhhh......-----------..hhhhhhhhhhhhheeeeee...hhhhh...hhhhhhhhh......hhhhhhhhhhh...eee.................eeeeeeee.-------.....ee.eeeee....hhhhhh.........eeeeeee.hhh.--..eeeee.hhh-------...eee......ee.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:79-541 (gaps) UniProt: 1-544 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                      Transcript 1
                 3sq8 C  79 GAVFKLMKSDFYERE-------DMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHhTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLS------DTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPP-----------ILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPARSKFYMHCATN-------SQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLA--RKVTCRTFTRD-------PTHVAVPFTLPVIPYDLAEDECFCLALH 541
                                    88    |    -  |    108       118       128       138       148       158       168       178   |   188       198       208       218       228       238       248       258       268       278       288     |   -  |    308       318       328       338  |      -    |  358       368       378       388       398       408       418       428       438   |     - |     458       468       478       488    |  498       | -     | 518       528       538   
                                         93     101                                                                              182-NEP                                                                                                         294    301                                     341         353                                                                                      442     450                                        493  |       506     514                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                           496                                             


Chain D from PDB  Type:PROTEIN  Length:425
 aligned with TYDP1_YEAST | P38319 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:464
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538    
          TYDP1_YEAST    79 GAVFKLMKSDFYEREDFMGEVEDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSAGTSASDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPAKDTAGRKKAEILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATNSAGPCDASQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDRRGCAGNPTHVAVPFTLPVIPYDLAEDECFCLARHE 542
               SCOP domains d3sq8d1 D:79-29       3 automated matches                                                                                                                                                                              d      3sq8d2 D:294-542 automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........-------.eehhhhhhh...eeeeeee...eehhhhhh.......eeeeeee...ee..hhhhhhhhhhhhhh.eeeeee...........eeeeee...eeeeeee....hhhhhhh...eeee...eee......hhhhhhhhhhhhh..hhhhhhhhhhhhhheehhhhh..eeeee.......hhhhhhhhhhhhh.------..eeeeeee..............hhhhhhhhhhhh......-----------..hhhhhhhhhhhhheeeeee...hhhhh...hhhhhhhhh......hhhhhhhhhhh...eee.................eeeeeeee.-------.....ee.eeeee....hhhhhh.........eeeeeee.hhh.-...eeeee.hhh-------...eee......ee.........hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:79-542 (gaps) UniProt: 1-544 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                       Transcript 1
                 3sq8 D  79 GAVFKLMKSDFYERE-------DMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHhTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLS------DTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPP-----------ILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPARSKFYMHCATN-------SQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLA-TRKVTCRTFTRD-------PTHVAVPFTLPVIPYDLAEDECFCLALHH 542
                                    88    |    -  |    108       118       128       138       148       158       168       178   |   188       198       208       218       228       238       248       258       268       278       288     |   -  |    308       318       328       338  |      -    |  358       368       378       388       398       408       418       428       438   |     - |     458       468       478       488    | |498       | -     | 518       528       538    
                                         93     101                                                                              182-NEP                                                                                                         294    301                                     341         353                                                                                      442     450                                        493 |        506     514                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                          495
   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, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SQ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SQ8)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TYDP1_YEAST | P38319)
molecular function
    GO:0017005    3'-tyrosyl-DNA phosphodiesterase activity    Catalysis of the hydrolysis of 3'-phosphotyrosyl groups formed as covalent intermediates (in DNA backbone breakage) between DNA topoisomerase I and DNA.
    GO:0070260    5'-tyrosyl-DNA phosphodiesterase activity    Catalysis of the hydrolysis of 5'-phosphotyrosyl groups formed as covalent intermediates (in DNA backbone breakage) between DNA topoisomerase II and DNA.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  Cis Peptide Bonds
    Leu A:523 - Pro A:524   [ RasMol ]  
    Leu B:523 - Pro B:524   [ RasMol ]  
    Leu C:523 - Pro C:524   [ RasMol ]  
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  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
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  3sq8
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  TYDP1_YEAST | P38319
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  3.1.4.-
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  TYDP1_YEAST | P38319
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 Related Entries

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

UniProtKB/Swiss-Prot
        TYDP1_YEAST | P38319: 1q32 3sq3 3sq5 3sq7

(-) Related Entries Specified in the PDB File

1q32 WILD TYPE STRUCTURE
3sq3
3sq5
3sq7