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Asym. Unit
Info
Asym.Unit (606 KB)
Biol.Unit 1 (206 KB)
Biol.Unit 2 (207 KB)
Biol.Unit 3 (206 KB)
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(1)
Title
:
STRUCTURAL BASIS OF MUTUAL ACTIVATION OF THE TRYPTOPHAN SYNTHASE A2B2 COMPLEX FROM A HYPERTHERMOPHILE, PYROCOCCUS FURIOSUS
Authors
:
S. J. Lee, K. Ogasahara, J. Ma, K. Nishio, M. Ishida, Y. Yamagata, T. Tsuk K. Yutani, Riken Structural Genomics/Proteomics Initiative (R
Date
:
19 May 04 (Deposition) - 12 Jul 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Keywords
:
Alpha/Beta, Alpha+Beta, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. J. Lee, K. Ogasahara, J. Ma, K. Nishio, M. Ishida, Y. Yamagata, T. Tsukihara, K. Yutani
Conformational Changes In The Tryptophan Synthase From A Hyperthermophile Upon Alpha(2)Beta(2) Complex Formation: Crystal Structure Of The Complex
Biochemistry V. 44 11417 2005
[
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Hetero Components
(1, 6)
Info
All Hetero Components
1a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
1b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
1c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
1d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
1e: PYRIDOXAL-5'-PHOSPHATE (PLPe)
1f: PYRIDOXAL-5'-PHOSPHATE (PLPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PLP
6
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS B:81 , LYS B:82 , GLN B:109 , SER B:185 , GLY B:227 , GLY B:228 , GLY B:229 , SER B:230 , ASN B:231 , GLY B:298 , GLU B:345 , SER B:371 , GLY B:372 , HOH B:412
BINDING SITE FOR RESIDUE PLP B 400
2
AC2
SOFTWARE
HIS D:81 , LYS D:82 , GLN D:109 , SER D:185 , GLY D:227 , GLY D:228 , GLY D:229 , SER D:230 , ASN D:231 , GLY D:298 , GLU D:345 , SER D:371 , GLY D:372 , HOH D:423
BINDING SITE FOR RESIDUE PLP D 400
3
AC3
SOFTWARE
HIS F:81 , LYS F:82 , GLN F:109 , SER F:185 , GLY F:227 , GLY F:228 , GLY F:229 , SER F:230 , ASN F:231 , GLY F:298 , GLU F:345 , SER F:371 , GLY F:372 , HOH F:433
BINDING SITE FOR RESIDUE PLP F 400
4
AC4
SOFTWARE
HIS H:81 , LYS H:82 , GLN H:109 , SER H:185 , GLY H:227 , GLY H:228 , GLY H:229 , SER H:230 , ASN H:231 , GLY H:298 , GLU H:345 , SER H:371 , GLY H:372 , HOH H:429
BINDING SITE FOR RESIDUE PLP H 400
5
AC5
SOFTWARE
HIS J:81 , LYS J:82 , GLN J:109 , SER J:185 , GLY J:227 , GLY J:228 , GLY J:229 , SER J:230 , ASN J:231 , GLY J:298 , GLU J:345 , SER J:371 , GLY J:372
BINDING SITE FOR RESIDUE PLP J 400
6
AC6
SOFTWARE
HIS L:81 , LYS L:82 , GLN L:109 , SER L:185 , GLY L:227 , GLY L:228 , GLY L:229 , SER L:230 , ASN L:231 , GLY L:298 , GLU L:345 , SER L:371 , GLY L:372 , HOH L:429
BINDING SITE FOR RESIDUE PLP L 400
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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]
PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: TRP_SYNTHASE_ALPHA (A:35-48,C:35-48,E:35-48,G:35-48,I:...)
2: TRP_SYNTHASE_BETA (B:75-89,D:75-89,F:75-89,H:75-89,J:...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRP_SYNTHASE_ALPHA
PS00167
Tryptophan synthase alpha chain signature.
TRPA_PYRFU
35-48
6
A:35-48
C:35-48
E:35-48
G:35-48
I:35-48
K:35-48
2
TRP_SYNTHASE_BETA
PS00168
Tryptophan synthase beta chain pyridoxal-phosphate attachment site.
TRPB1_PYRFU
75-89
6
B:75-89
D:75-89
F:75-89
H:75-89
J:75-89
L:75-89
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1wdwa_ (A:)
1b: SCOP_d1wdwc_ (C:)
1c: SCOP_d1wdwe_ (E:)
1d: SCOP_d1wdwg_ (G:)
1e: SCOP_d1wdwi_ (I:)
1f: SCOP_d1wdwk_ (K:)
2a: SCOP_d1wdwb_ (B:)
2b: SCOP_d1wdwd_ (D:)
2c: SCOP_d1wdwf_ (F:)
2d: SCOP_d1wdwh_ (H:)
2e: SCOP_d1wdwj_ (J:)
2f: SCOP_d1wdwl_ (L:)
View:
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)
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)
Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Ribulose-phoshate binding barrel
(356)
Family
:
Tryptophan biosynthesis enzymes
(108)
Protein domain
:
Trp synthase alpha-subunit
(62)
Pyrococcus furiosus [TaxId: 2261]
(10)
1a
d1wdwa_
A:
1b
d1wdwc_
C:
1c
d1wdwe_
E:
1d
d1wdwg_
G:
1e
d1wdwi_
I:
1f
d1wdwk_
K:
Fold
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(165)
Superfamily
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(165)
Family
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(120)
Protein domain
:
Tryptophan synthase, beta-subunit
(45)
Pyrococcus furiosus [TaxId: 2261]
(2)
2a
d1wdwb_
B:
2b
d1wdwd_
D:
2c
d1wdwf_
F:
2d
d1wdwh_
H:
2e
d1wdwj_
J:
2f
d1wdwl_
L:
[
close SCOP info
]
CATH Domains
(2, 18)
Info
all CATH domains
1a: CATH_1wdwB01 (B:3-47,B:82-200)
1b: CATH_1wdwB02 (B:48-81,B:201-385)
1c: CATH_1wdwD02 (D:48-81,D:201-385)
1d: CATH_1wdwF02 (F:48-81,F:201-385)
1e: CATH_1wdwH02 (H:48-81,H:201-385)
1f: CATH_1wdwJ02 (J:48-81,J:201-385)
1g: CATH_1wdwL02 (L:48-81,L:201-385)
1h: CATH_1wdwD01 (D:3-47,D:82-200)
1i: CATH_1wdwF01 (F:3-47,F:82-200)
1j: CATH_1wdwH01 (H:3-47,H:82-200)
1k: CATH_1wdwJ01 (J:3-47,J:82-200)
1l: CATH_1wdwL01 (L:3-47,L:82-200)
2a: CATH_1wdwE00 (E:1-248)
2b: CATH_1wdwI00 (I:1-248)
2c: CATH_1wdwG00 (G:1-248)
2d: CATH_1wdwA00 (A:1-247)
2e: CATH_1wdwC00 (C:1-248)
2f: CATH_1wdwK00 (K:1-248)
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)
Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1100, no name defined]
(77)
Pyrococcus furiosus. Organism_taxid: 2261.
(2)
1a
1wdwB01
B:3-47,B:82-200
1b
1wdwB02
B:48-81,B:201-385
1c
1wdwD02
D:48-81,D:201-385
1d
1wdwF02
F:48-81,F:201-385
1e
1wdwH02
H:48-81,H:201-385
1f
1wdwJ02
J:48-81,J:201-385
1g
1wdwL02
L:48-81,L:201-385
1h
1wdwD01
D:3-47,D:82-200
1i
1wdwF01
F:3-47,F:82-200
1j
1wdwH01
H:3-47,H:82-200
1k
1wdwJ01
J:3-47,J:82-200
1l
1wdwL01
L:3-47,L:82-200
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Pyrococcus furiosus. Organism_taxid: 2261.
(11)
2a
1wdwE00
E:1-248
2b
1wdwI00
I:1-248
2c
1wdwG00
G:1-248
2d
1wdwA00
A:1-247
2e
1wdwC00
C:1-248
2f
1wdwK00
K:1-248
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Trp_syntA_1wdwK01 (K:2-246)
1b: PFAM_Trp_syntA_1wdwK02 (K:2-246)
1c: PFAM_Trp_syntA_1wdwK03 (K:2-246)
1d: PFAM_Trp_syntA_1wdwK04 (K:2-246)
1e: PFAM_Trp_syntA_1wdwK05 (K:2-246)
1f: PFAM_Trp_syntA_1wdwK06 (K:2-246)
2a: PFAM_PALP_1wdwL01 (L:45-372)
2b: PFAM_PALP_1wdwL02 (L:45-372)
2c: PFAM_PALP_1wdwL03 (L:45-372)
2d: PFAM_PALP_1wdwL04 (L:45-372)
2e: PFAM_PALP_1wdwL05 (L:45-372)
2f: PFAM_PALP_1wdwL06 (L:45-372)
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Clans
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)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
Trp_syntA
(28)
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
(1)
1a
Trp_syntA-1wdwK01
K:2-246
1b
Trp_syntA-1wdwK02
K:2-246
1c
Trp_syntA-1wdwK03
K:2-246
1d
Trp_syntA-1wdwK04
K:2-246
1e
Trp_syntA-1wdwK05
K:2-246
1f
Trp_syntA-1wdwK06
K:2-246
Clan
:
no clan defined [family: PALP]
(67)
Family
:
PALP
(67)
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
(2)
2a
PALP-1wdwL01
L:45-372
2b
PALP-1wdwL02
L:45-372
2c
PALP-1wdwL03
L:45-372
2d
PALP-1wdwL04
L:45-372
2e
PALP-1wdwL05
L:45-372
2f
PALP-1wdwL06
L:45-372
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