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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE YEAST TYROSYL-DNA PHOSPHODIESTERASE
 
Authors :  X. He, K. Babaoglu, A. Price, K. C. Nitiss, J. L. Nitiss, S. W. White
Date :  28 Jul 03  (Deposition) - 07 Sep 04  (Release) - 10 Jun 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
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)
Keywords :  Tyrosyl-Dna Phosphodiesterase; Tdp; Dna Repair, Replication, Transcription, Hydrolase, Replication, Transcription, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. He, R. C. Van Waardenburg, K. Babaoglu, A. C. Price, K. C. Nitiss, J. L. Nitiss, M. A. Bjornsti, S. W. White
Mutation Of A Conserved Active Site Residue Converts Tyrosyl-Dna Phosphodiesterase I Into A Dna Topoisomerase I-Dependent Poison
J. Mol. Biol. V. 372 1070 2007
PubMed-ID: 17707402  |  Reference-DOI: 10.1016/J.JMB.2007.07.055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSYL-DNA PHOSPHODIESTERASE
    Chains: A, B, C, D
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-23B (NOVAGEN)
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TDP1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: TYROSINE-DNA PHOSPHODIESTERASE;
TDP1P

 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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Q32)

(-) Sites  (0, 0)

(no "Site" information available for 1Q32)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q32)

(-) 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 1Q32)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q32)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR223C1YBR223C.1II:670292-6686581635TYDP1_YEAST1-5445444A:79-538 (gaps)
B:79-540 (gaps)
C:79-541 (gaps)
D:79-538 (gaps)		460
462
463
460

(-) 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:419
 aligned with TYDP1_YEAST | P38319 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:460
                                    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 GAVFKLMKSDFYEREDFMGEVEDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSAGTSASDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPAKDTAGRKKAEILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATNSAGPCDASQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDRRGCAGNPTHVAVPFTLPVIPYDLAEDECFCL 538
               SCOP domains d1q32a1 A:79-29       3 Tyrosyl-DNA phosphodiesterase TDP1                                                                                                                                                             -      -d1q32a2 A:302-538 Tyrosyl-DNA phosphodie           sterase TDP1                                                                                                                                                                               SCOP domains
               CATH domains 1q32A01 A:79-26       7 Endonuclease Chain A                                                                                                                                                 1q32A02 A:268-538 Phospholi      pase D/nuclease; domain 2                                                                                                                                                                                                                      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..............hhhhhhhhhhhhh.....-----------..hhhhhhhhhhhhheeeeee...hhhhh...hhhhhhhhh...hhhhhhhhhhhhhh...eee.................eeeeeeee.-------.....ee.eeeee....hhhhhh.........eeeeeee.hhh---..eeeee.hhh-------...eee......ee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:79-538 (gaps) UniProt: 1-544 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 1q32 A  79 GAVFKLMKSDFYERE-------DMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLS------DTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPP-----------ILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATN-------SQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRL---RKVTCRTFTRD-------PTHVAVPFTLPVIPYDLAEDECFCL 538
                                    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                                                                                                                                                                                              294    301                                     341         353                                                                                      442     450                                       492 496       506     514                        


Chain B from PDB  Type:PROTEIN  Length:420
 aligned with TYDP1_YEAST | P38319 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:462
                                    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 GAVFKLMKSDFYEREDFMGEVEDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSAGTSASDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPAKDTAGRKKAEILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATNSAGPCDASQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDRRGCAGNPTHVAVPFTLPVIPYDLAEDECFCLAR 540
               SCOP domains d1q32b1 B:79-2         93 Tyrosyl-DNA phosphodiesterase TDP1                                                                                                                                                           -      -d1q32b2 B:302-538 Tyrosyl-DNA phosphod             iesterase TDP1                                                                                                                                                                            -- SCOP domains
               CATH domains 1q32B01 B:79-2         67 Endonuclease Chain A                                                                                                                                               1q32B02 B:268-540 Phospholi      pase D/nuclease; domain 2                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee........---------..hhhhhhh...eeeeeee...eehhhhhh.......eeeeeee...ee.......hhhhhhhhh.eeeeee...........eeeeee...eeeeeee....hhhhhhh...eeee...eee......hhhhhhhhhhhhh..hhhhhhhhhhhhhheehhhhh..eeeee.......hhhhhhhhhhhhhh------..eeeeeee..............hhhhhhhhhhhhh...-------------..hhhhhhhhhhhhheeeeee...hhhhh...hhhhhhhhh...hhhhhhhhhhhhhh...eee.................eeeeeeee-------......ee.eeeee....hhhhhh.........eeeeeee.hhh.....eeeee.hhh-------...eee......ee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:79-540 (gaps) UniProt: 1-544 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 1q32 B  79 GAVFKLMKSDFYER---------MITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLS------DTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMS-------------ILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCAT-------ASQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRD-------PTHVAVPFTLPVIPYDLAEDECFCLAR 540
                                    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  
                                        92       102                                                                                                                                                                                             294    301                                   339           353                                                                                     441     449                                                      506     514                          


Chain C from PDB  Type:PROTEIN  Length:417
 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 d1q32c1 C:79-        293 Tyrosyl-DNA phosphodiesterase TDP1                                                                                                                                                                    d1q32c2 C:302-538 Tyrosyl-DNA phosphodi            esterase TDP1                                                                                                                                                                             --- SCOP domains
               CATH domains 1q32C01 C:79-        267 Endonuclease Chain A                                                                                                                                                1q32C02 C:268-541 Phosphol        ipase D/nuclease; domain 2                                                                                                                                                                                                                       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.......hhhhhhhhhhhhh--------..eeeeee..............hhhhhhhhhhhhh....------------..hhhhhhhhhhhhheeeeee...hhhhh...hhhhhhhhh...hhhhhhhhhhhhhh...eee.................eeeeeee.-----------..ee.eeeee....hhhhhh.........eeeeeee.hhh.....eeeee.hhh-------...eee......ee.............. 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
                 1q32 C  79 GAVFKLMKSDFYE--------EDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKL--------TAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSP------------ILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCAT-----------FKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRD-------PTHVAVPFTLPVIPYDLAEDECFCLARH 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   
                                       91      100                                                                                                                                                                                              293      302                                   340          353                                                                                     441         453                                                  506     514                           


Chain D from PDB  Type:PROTEIN  Length:415
 aligned with TYDP1_YEAST | P38319 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:460
                                    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 GAVFKLMKSDFYEREDFMGEVEDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSAGTSASDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPAKDTAGRKKAEILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATNSAGPCDASQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDRRGCAGNPTHVAVPFTLPVIPYDLAEDECFCL 538
               SCOP domains d1q32d1 D:79-          293 Tyrosyl-DNA phosphodiesterase TDP1                                                                                                                                                          -     --d1q32d2 D:302-538 Tyrosyl-DNA phosphodi            esterase TDP1                                                                                                                                                                              SCOP domains
               CATH domains 1q32D01 D:79-          267 Endonuclease Chain A                                                                                                                                              1q32D02 D:268-538 Phospholi     pase D/nuclease; domain 2                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) --Tyr-DNA_pho          spho-1q32D01 D:81-529                                                                                                                                                                                                                                                                                                                                                                                                                       --------- Pfam domains (1)
           Pfam domains (2) --Tyr-DNA_pho          spho-1q32D02 D:81-529                                                                                                                                                                                                                                                                                                                                                                                                                       --------- Pfam domains (2)
           Pfam domains (3) --Tyr-DNA_pho          spho-1q32D03 D:81-529                                                                                                                                                                                                                                                                                                                                                                                                                       --------- Pfam domains (3)
           Pfam domains (4) --Tyr-DNA_pho          spho-1q32D04 D:81-529                                                                                                                                                                                                                                                                                                                                                                                                                       --------- Pfam domains (4)
         Sec.struct. author ..eeee.......----------..hhhhhhh...eeeeeee...eehhhhhh.......eeeeeee...ee..hhhhhhhhhhhhh..eeeeee...........eeeeee...eeeeeee....hhhhhhh...eeee...eee......hhhhhhhhhhhhh..hhhhhhhhhhhhhheehhhhh..eeeee.......hhhhhhhhhhhhh.-----....eeeeee..............hhhhhhhhhhhhh....------------..hhhhhhhhhhhhheeeeee...hhhhh...hhhhhhhhh...hhhhhhhhhhhhhh...eee.................eeeeeee.---------....ee.eeeee....hhhhhh.........eeeeeee.hhh--...eeeee.hhh-------...eee......ee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:79-538 (gaps) UniProt: 1-544 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 1q32 D  79 GAVFKLMKSDFYE----------MITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLS-----SDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSP------------ILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCAT---------QVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRL--TRKVTCRTFTRD-------PTHVAVPFTLPVIPYDLAEDECFCL 538
                                    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
                                       91        102                                                                                                                                                                                             294   300                                     340          353                                                                                     441       451                                      492  |        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  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PLD (22)

(-) 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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    Leu A:523 - Pro A:524   [ RasMol ]  
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  1q32
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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

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        TYDP1_YEAST | P38319: 3sq3 3sq5 3sq7 3sq8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Q32)