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1UM2
Asym. Unit
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Asym.Unit (145 KB)
Biol.Unit 1 (71 KB)
Biol.Unit 2 (72 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE WITH THE LIGATED EXTEIN SEGMENT
Authors
:
R. Mizutani, Y. Anraku, Y. Satow
Date
:
22 Sep 03 (Deposition) - 22 Sep 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Protein Splicing, Vma1-Derived Endonuclease, Vde, Intein, Extein, Thiazolidine, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Mizutani, Y. Anraku, Y. Satow
Protein Splicing Of Yeast Vma1-Derived Endonuclease Via Thiazolidine Intermediates.
J. Synchrotron Radiat. V. 11 109 2004
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
Info
All Hetero Components
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Sorry, no Info available
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Sites
(0, 0)
Info
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: INTEIN_N_TER (A:285-366,B:285-366)
2: INTEIN_ENDONUCLEASE (A:494-642,B:494-642)
3: INTEIN_C_TER (A:713-737,B:713-737)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTEIN_N_TER
PS50817
Intein N-terminal splicing motif profile.
VATA_YEAST
284-366
2
A:285-366
B:285-366
2
INTEIN_ENDONUCLEASE
PS50819
Intein DOD-type homing endonuclease domain profile.
VATA_YEAST
494-642
2
A:494-642
B:494-642
3
INTEIN_C_TER
PS50818
Intein C-terminal splicing motif profile.
VATA_YEAST
713-738
2
A:713-737
B:713-737
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Exons
(1, 4)
Info
All Exons
Exon 1.1 (A:284-737 (gaps) | B:284-737 (gaps...)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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Note:
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
YDL185W
1
YDL185W.1
IV:126788-130003
3216
VATA_YEAST
1-1071
1071
4
A:284-737 (gaps)
B:284-737 (gaps)
C:281-741 (gaps)
D:281-741 (gaps)
454
454
28
28
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SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1um2a1 (A:284-463,A:699-737)
1b: SCOP_d1um2b1 (B:284-463,B:699-737)
2a: SCOP_d1um2a2 (A:464-581)
2b: SCOP_d1um2a3 (A:582-698)
2c: SCOP_d1um2b2 (B:464-581)
2d: SCOP_d1um2b3 (B:582-698)
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Organisms
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Class
:
All beta proteins
(24004)
Fold
:
Hedgehog/intein (Hint) domain
(16)
Superfamily
:
Hedgehog/intein (Hint) domain
(16)
Family
:
Intein (protein splicing domain)
(12)
Protein domain
:
VMA1-derived endonuclease (VDE) PI-Scei intein
(8)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(8)
1a
d1um2a1
A:284-463,A:699-737
1b
d1um2b1
B:284-463,B:699-737
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Homing endonuclease-like
(42)
Superfamily
:
Homing endonucleases
(38)
Family
:
Intein endonuclease
(8)
Protein domain
:
VMA1-derived endonuclease (VDE) PI-SceI
(7)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
2a
d1um2a2
A:464-581
2b
d1um2a3
A:582-698
2c
d1um2b2
B:464-581
2d
d1um2b3
B:582-698
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1um2B02 (B:466-586)
1b: CATH_1um2A02 (A:466-586)
1c: CATH_1um2B03 (B:587-681)
1d: CATH_1um2A03 (A:587-681)
2a: CATH_1um2B01 (B:284-462,B:699-737)
2b: CATH_1um2A01 (A:284-462,A:699-737)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Endonuclease I-creI
(41)
Homologous Superfamily
:
Homing endonucleases
(40)
Baker's yeast (Saccharomyces cerevisiae)
(8)
1a
1um2B02
B:466-586
1b
1um2A02
A:466-586
1c
1um2B03
B:587-681
1d
1um2A03
A:587-681
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Endonuclease - Pi-scei; Chain A, domain 1
(12)
Homologous Superfamily
:
Endonuclease - Pi-scei; Chain A, domain 1
(12)
Baker's yeast (Saccharomyces cerevisiae)
(6)
2a
1um2B01
B:284-462,B:699-737
2b
1um2A01
A:284-462,A:699-737
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Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_Hom_end_hint_1um2B01 (B:285-737)
1b: PFAM_Hom_end_hint_1um2B02 (B:285-737)
2a: PFAM_Hom_end_1um2B03 (B:585-696)
2b: PFAM_Hom_end_1um2B04 (B:585-696)
2c: PFAM_Hom_end_1um2B05 (B:585-696)
2d: PFAM_Hom_end_1um2B06 (B:585-696)
3a: PFAM_ATP_synt_ab_1um2B07 (B:285-737)
3b: PFAM_ATP_synt_ab_1um2B08 (B:285-737)
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Clan
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H-int
(15)
Family
:
Hom_end_hint
(5)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(5)
1a
Hom_end_hint-1um2B01
B:285-737
1b
Hom_end_hint-1um2B02
B:285-737
Clan
:
Homing_endonuc
(19)
Family
:
Hom_end
(5)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(5)
2a
Hom_end-1um2B03
B:585-696
2b
Hom_end-1um2B04
B:585-696
2c
Hom_end-1um2B05
B:585-696
2d
Hom_end-1um2B06
B:585-696
Clan
:
P-loop_NTPase
(1112)
Family
:
ATP-synt_ab
(44)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(11)
3a
ATP-synt_ab-1um2B07
B:285-737
3b
ATP-synt_ab-1um2B08
B:285-737
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