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1PVY
Asym. Unit
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Asym.Unit (85 KB)
Biol.Unit 1 (80 KB)
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(1)
Title
:
3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE FROM M. JANNASCHII IN COMPLEX WITH RIBULOSE 5-PHOSPHATE
Authors
:
S. Steinbacher, S. Schiffmann, G. Richter, R. Huber, A. Bacher, M. Fischer
Date
:
29 Jun 03 (Deposition) - 04 Nov 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Riboflavin Biosynthesis, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Steinbacher, S. Schiffmann, G. Richter, R. Huber, A. Bacher, M. Fischer
Structure Of 3, 4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii In Complex With Divalent Metal Ions And The Substrate Ribulose 5-Phosphate: Implications For The Catalytic Mechanism
J. Biol. Chem. V. 278 42256 2003
(for further references see the
PDB file header
)
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: RIBULOSE-5-PHOSPHATE (5RPa)
1b: RIBULOSE-5-PHOSPHATE (5RPb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
5RP
2
Ligand/Ion
RIBULOSE-5-PHOSPHATE
2
CA
4
Ligand/Ion
CALCIUM ION
3
ZN
3
Ligand/Ion
ZINC ION
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:25 , GLU A:26 , ASP A:30 , CYS A:55 , TYR A:95 , LEU A:151 , ARG A:161 , GLY A:163 , HIS A:164 , THR A:165 , ILE A:183 , GLU A:185 , ZN A:502 , CA A:503 , HOH A:723 , HOH A:766 , HOH A:847 , HOH A:851 , HOH A:852
BINDING SITE FOR RESIDUE 5RP A 501
2
AC2
SOFTWARE
ARG B:25 , GLU B:26 , ASP B:30 , CYS B:55 , PHE B:101 , ARG B:161 , GLY B:163 , HIS B:164 , THR B:165 , GLU B:185 , ZN B:602 , CA B:603 , HOH B:772 , HOH B:778 , HOH B:785 , HOH B:804 , HOH B:805 , HOH B:806
BINDING SITE FOR RESIDUE 5RP B 601
3
AC3
SOFTWARE
GLU A:26 , HIS A:164 , 5RP A:501 , HOH A:852
BINDING SITE FOR RESIDUE ZN A 502
4
AC4
SOFTWARE
GLU A:26 , TYR A:95 , 5RP A:501 , HOH A:851
BINDING SITE FOR RESIDUE CA A 503
5
AC5
SOFTWARE
GLU B:26 , HIS B:164 , 5RP B:601 , HOH B:805
BINDING SITE FOR RESIDUE ZN B 602
6
AC6
SOFTWARE
GLU B:26 , 5RP B:601 , HOH B:764 , HOH B:804 , HOH B:806
BINDING SITE FOR RESIDUE CA B 603
7
AC7
SOFTWARE
ASP A:96 , GLU A:97 , HOH A:753 , HOH A:769 , HOH A:774 , HOH A:806
BINDING SITE FOR RESIDUE CA A 701
8
AC8
SOFTWARE
GLU A:204 , ASN A:207 , HOH A:787 , HOH B:613 , HOH B:655
BINDING SITE FOR RESIDUE CA A 702
9
AC9
SOFTWARE
HIS A:206
BINDING SITE FOR RESIDUE ZN A 703
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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
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1pvya_ (A:)
1b: SCOP_d1pvyb_ (B:)
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Protein Domains
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Organisms
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(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
YrdC/RibB
(27)
Superfamily
:
YrdC/RibB
(27)
Family
:
3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB
(19)
Protein domain
:
3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB
(13)
Methanocaldococcus jannaschii [TaxId: 2190]
(3)
1a
d1pvya_
A:
1b
d1pvyb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1pvyA00 (A:2-220)
1b: CATH_1pvyB00 (B:3-221)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
DHBP synthase
(20)
Homologous Superfamily
:
DHBP synthase
(20)
Methanocaldococcus jannaschii. Organism_taxid: 2190.
(3)
1a
1pvyA00
A:2-220
1b
1pvyB00
B:3-221
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_DHBP_synthase_1pvyB01 (B:4-220)
1b: PFAM_DHBP_synthase_1pvyB02 (B:4-220)
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Clan
:
no clan defined [family: DHBP_synthase]
(17)
Family
:
DHBP_synthase
(17)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(3)
1a
DHBP_synthase-1pvyB01
B:4-220
1b
DHBP_synthase-1pvyB02
B:4-220
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Asymmetric Unit 1
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