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1Q32
Asym. Unit
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Asym.Unit (300 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (79 KB)
Biol.Unit 3 (77 KB)
Biol.Unit 4 (76 KB)
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(1)
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:
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Gene Ontology, PubMed, Web (Google)
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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
(for further references see the
PDB file header
)
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Hetero Components
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Sites
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Exons
(1, 4)
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All Exons
Exon 1.1 (A:79-538 (gaps) | B:79-540 (gaps) ...)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YBR223C
1
YBR223C.1
II:670292-668658
1635
TYDP1_YEAST
1-544
544
4
A:79-538 (gaps)
B:79-540 (gaps)
C:79-541 (gaps)
D:79-538 (gaps)
460
462
463
460
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SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1q32a1 (A:79-293)
1b: SCOP_d1q32a2 (A:302-538)
1c: SCOP_d1q32b1 (B:79-293)
1d: SCOP_d1q32b2 (B:302-538)
1e: SCOP_d1q32c1 (C:79-293)
1f: SCOP_d1q32c2 (C:302-538)
1g: SCOP_d1q32d1 (D:79-293)
1h: SCOP_d1q32d2 (D:302-538)
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Protein Domains
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Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Phospholipase D/nuclease
(33)
Superfamily
:
Phospholipase D/nuclease
(33)
Family
:
Tyrosyl-DNA phosphodiesterase TDP1
(17)
Protein domain
:
Tyrosyl-DNA phosphodiesterase TDP1
(13)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
1a
d1q32a1
A:79-293
1b
d1q32a2
A:302-538
1c
d1q32b1
B:79-293
1d
d1q32b2
B:302-538
1e
d1q32c1
C:79-293
1f
d1q32c2
C:302-538
1g
d1q32d1
D:79-293
1h
d1q32d2
D:302-538
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1q32A01 (A:79-267)
1b: CATH_1q32C01 (C:79-267)
1c: CATH_1q32B01 (B:79-267)
1d: CATH_1q32D01 (D:79-267)
2a: CATH_1q32A02 (A:268-538)
2b: CATH_1q32C02 (C:268-541)
2c: CATH_1q32D02 (D:268-538)
2d: CATH_1q32B02 (B:268-540)
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Class
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Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Endonuclease; Chain A
(28)
Homologous Superfamily
:
Endonuclease Chain A
(28)
Baker's yeast (Saccharomyces cerevisiae)
(1)
1a
1q32A01
A:79-267
1b
1q32C01
C:79-267
1c
1q32B01
B:79-267
1d
1q32D01
D:79-267
Homologous Superfamily
:
Phospholipase D/nuclease; domain 2
(13)
Baker's yeast (Saccharomyces cerevisiae)
(1)
2a
1q32A02
A:268-538
2b
1q32C02
C:268-541
2c
1q32D02
D:268-538
2d
1q32B02
B:268-540
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Tyr_DNA_phospho_1q32D01 (D:81-529)
1b: PFAM_Tyr_DNA_phospho_1q32D02 (D:81-529)
1c: PFAM_Tyr_DNA_phospho_1q32D03 (D:81-529)
1d: PFAM_Tyr_DNA_phospho_1q32D04 (D:81-529)
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Clan
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PLD
(22)
Family
:
Tyr-DNA_phospho
(11)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
1a
Tyr-DNA_phospho-1q32D01
D:81-529
1b
Tyr-DNA_phospho-1q32D02
D:81-529
1c
Tyr-DNA_phospho-1q32D03
D:81-529
1d
Tyr-DNA_phospho-1q32D04
D:81-529
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Asym.Unit (300 KB)
Header - Asym.Unit
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Biol.Unit 3 (77 KB)
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