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(1)
Title
:
CRYSTAL STRUCTURE OF DNA PHOTOLYASE FROM THERMUS THERMOPHILUS
Authors
:
H. Komori, R. Masui, S. Kuramitsu, S. Yokoyama, T. Shibata, Y. Inoue, K. Miki
Date
:
27 Jul 01 (Deposition) - 28 Nov 01 (Release) - 01 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Dna Repair, Cyclobutane Pyrimidine Dimer (Cpd), Fad, Photoreactivating Enzyme, Dna-Binding, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Komori, R. Masui, S. Kuramitsu, S. Yokoyama, T. Shibata, Y. Inoue, K. Miki
Crystal Structure Of Thermostable Dna Photolyase: Pyrimidine-Dimer Recognition Mechanism.
Proc. Natl. Acad. Sci. Usa V. 98 13560 2001
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2a: PHOSPHATE ION (PO4a)
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No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
PO4
1
Ligand/Ion
PHOSPHATE ION
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:9 , GLY A:10 , SER A:96 , ARG A:104 , HOH A:424
BINDING SITE FOR RESIDUE PO4 A 422
2
AC2
SOFTWARE
TYR A:197 , GLY A:209 , SER A:210 , ARG A:211 , LEU A:212 , SER A:213 , PHE A:216 , TRP A:241 , GLU A:244 , TRP A:247 , ARG A:248 , PHE A:307 , LEU A:308 , ASN A:310 , ARG A:313 , ALA A:317 , LEU A:339 , ASP A:341 , GLY A:342 , ASP A:343 , VAL A:346 , ASN A:347 , GLN A:349 , GLY A:350 , HOH A:440 , HOH A:457 , HOH A:475 , HOH A:494
BINDING SITE FOR RESIDUE FAD A 421
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PHR_CRY_ALPHA_BETA (A:2-124)
2: DNA_PHOTOLYASES_1_1 (A:290-302)
3: DNA_PHOTOLYASES_1_2 (A:310-329)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHR_CRY_ALPHA_BETA
PS51645
Photolyase/cryptochrome alpha/beta domain profile.
PHR_THET8
2-124
1
A:2-124
2
DNA_PHOTOLYASES_1_1
PS00394
DNA photolyases class 1 signature 1.
PHR_THET8
290-302
1
A:290-302
3
DNA_PHOTOLYASES_1_2
PS00691
DNA photolyases class 1 signature 2.
PHR_THET8
310-329
1
A:310-329
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1iqra1 (A:172-416)
2a: SCOP_d1iqra2 (A:2-171)
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cryptochrome/photolyase FAD-binding domain
(26)
Superfamily
:
Cryptochrome/photolyase FAD-binding domain
(26)
Family
:
Cryptochrome/photolyase FAD-binding domain
(20)
Protein domain
:
C-terminal domain of DNA photolyase
(13)
Thermus thermophilus [TaxId: 274]
(5)
1a
d1iqra1
A:172-416
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Cryptochrome/photolyase, N-terminal domain
(27)
Superfamily
:
Cryptochrome/photolyase, N-terminal domain
(27)
Family
:
Cryptochrome/photolyase, N-terminal domain
(17)
Protein domain
:
DNA photolyase
(13)
Thermus thermophilus [TaxId: 274]
(5)
2a
d1iqra2
A:2-171
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1iqrA01 (A:2-121)
2a: CATH_1iqrA02 (A:122-149,A:179-258)
3a: CATH_1iqrA03 (A:259-416)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Thermus thermophilus. Organism_taxid: 274.
(11)
1a
1iqrA01
A:2-121
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha Horseshoe
(399)
Topology
:
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
(320)
Homologous Superfamily
:
[code=1.25.40.80, no name defined]
(16)
Thermus thermophilus. Organism_taxid: 274.
(2)
2a
1iqrA02
A:122-149,A:179-258
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
(16)
Homologous Superfamily
:
DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3
(16)
Thermus thermophilus. Organism_taxid: 274.
(2)
3a
1iqrA03
A:259-416
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Pfam Domains
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Asymmetric Unit 1
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