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1PG8
Asym. Unit
Info
Asym.Unit (258 KB)
Biol.Unit 1 (252 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF L-METHIONINE ALPHA-, GAMMA-LYASE
Authors
:
T. W. Allen, V. Sridhar, G. S. Prasad, Q. Han, M. Xu, Y. Tan, R. M. Hoffman, S. Ramaswamy
Date
:
28 May 03 (Deposition) - 08 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.68
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Lyase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
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Hetero Components
(3, 19)
Info
All Hetero Components
1a: DI(HYDROXYETHYL)ETHER (PEGa)
1b: DI(HYDROXYETHYL)ETHER (PEGb)
1c: DI(HYDROXYETHYL)ETHER (PEGc)
1d: DI(HYDROXYETHYL)ETHER (PEGd)
1e: DI(HYDROXYETHYL)ETHER (PEGe)
1f: DI(HYDROXYETHYL)ETHER (PEGf)
1g: DI(HYDROXYETHYL)ETHER (PEGg)
1h: DI(HYDROXYETHYL)ETHER (PEGh)
1i: DI(HYDROXYETHYL)ETHER (PEGi)
1j: DI(HYDROXYETHYL)ETHER (PEGj)
1k: DI(HYDROXYETHYL)ETHER (PEGk)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
2b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
2c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
2d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PEG
11
Ligand/Ion
DI(HYDROXYETHYL)ETHER
2
PLP
4
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
3
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(19, 19)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR C:114 , LYS C:211 , VAL C:339 , SER C:340 , GLN C:349 , ARG C:375 , HOH C:1284 , HOH C:1285
BINDING SITE FOR RESIDUE SO4 C 1146
02
AC2
SOFTWARE
TYR A:114 , ASN A:161 , LYS A:211 , VAL A:339 , SER A:340 , ARG A:375 , HOH A:1495 , HOH A:1496
BINDING SITE FOR RESIDUE SO4 A 1124
03
AC3
SOFTWARE
TYR B:114 , LYS B:211 , VAL B:339 , SER B:340 , LEU B:341 , GLN B:349 , ARG B:375 , PLP B:1799
BINDING SITE FOR RESIDUE SO4 B 1138
04
AC4
SOFTWARE
TYR D:114 , LYS D:211 , VAL D:339 , SER D:340 , GLN D:349 , ARG D:375
BINDING SITE FOR RESIDUE SO4 D 1147
05
AC5
SOFTWARE
SER A:88 , GLY A:89 , MET A:90 , ILE A:93 , TYR A:114 , ASP A:186 , SER A:208 , THR A:210 , LYS A:211 , HOH A:1495 , TYR C:59 , ARG C:61
BINDING SITE FOR RESIDUE PLP A 1399
06
AC6
SOFTWARE
SER B:88 , GLY B:89 , MET B:90 , TYR B:114 , ASP B:186 , TYR B:189 , SER B:208 , THR B:210 , LYS B:211 , LEU B:341 , SO4 B:1138 , TYR D:59 , ARG D:61
BINDING SITE FOR RESIDUE PLP B 1799
07
AC7
SOFTWARE
TYR A:59 , ARG A:61 , SER C:88 , GLY C:89 , MET C:90 , TYR C:114 , ASP C:186 , TYR C:189 , SER C:208 , THR C:210 , LYS C:211 , HOH C:1284
BINDING SITE FOR RESIDUE PLP C 1199
08
AC8
SOFTWARE
TYR B:59 , ARG B:61 , SER D:88 , GLY D:89 , MET D:90 , TYR D:114 , ASP D:186 , THR D:188 , TYR D:189 , SER D:208 , THR D:210 , LYS D:211 , LEU D:341
BINDING SITE FOR RESIDUE PLP D 1599
09
AC9
SOFTWARE
SER A:4 , LYS A:6 , PEG A:1002 , HOH A:1404 , ASP D:385
BINDING SITE FOR RESIDUE PEG A 1001
10
BC1
SOFTWARE
PRO A:8 , THR A:12 , ARG A:13 , HIS A:17 , PEG A:1001 , PEG A:1003 , HOH A:1404 , HOH A:1499
BINDING SITE FOR RESIDUE PEG A 1002
11
BC2
SOFTWARE
HIS A:16 , TYR A:19 , PEG A:1002
BINDING SITE FOR RESIDUE PEG A 1003
12
BC3
SOFTWARE
HIS A:24 , TYR A:33 , HIS A:57 , GLY B:25
BINDING SITE FOR RESIDUE PEG A 1004
13
BC4
SOFTWARE
GLY A:25 , HIS B:24
BINDING SITE FOR RESIDUE PEG A 1005
14
BC5
SOFTWARE
GLY B:18 , TYR B:19 , HIS B:24 , PRO B:30 , PRO B:31 , VAL B:32 , PRO B:65 , THR B:66
BINDING SITE FOR RESIDUE PEG B 1006
15
BC6
SOFTWARE
ALA A:295 , SER A:296 , PHE A:297 , PRO A:298 , TYR A:300 , THR A:301 , ALA C:271 , GLN C:274 , VAL C:275 , GLU C:278 , HOH C:1281
BINDING SITE FOR RESIDUE PEG A 1007
16
BC7
SOFTWARE
GLY A:110 , ASN A:111 , THR A:112 , LEU A:113 , VAL A:135 , ASP A:136 , MET A:137 , PHE A:156 , GLU A:157 , ALA A:160 , HIS A:165 , HOH A:1431
BINDING SITE FOR RESIDUE PEG A 1008
17
BC8
SOFTWARE
ALA B:11 , ASN B:263 , ARG C:268 , ASN C:272 , LEU C:380 , GLU C:381 , ASP C:382 , ILE C:383 , HOH C:1265
BINDING SITE FOR RESIDUE PEG C 1009
18
BC9
SOFTWARE
PRO B:8 , HIS B:17
BINDING SITE FOR RESIDUE PEG B 1010
19
CC1
SOFTWARE
HIS B:16 , ASP B:20 , GLN C:333 , LEU C:334 , SER C:336 , HOH C:1216
BINDING SITE FOR RESIDUE PEG C 1012
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: CYS_MET_METAB_PP (A:203-217,B:203-217,C:203-217,D:20...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYS_MET_METAB_PP
PS00868
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.
MEGL_PSEPU
203-217
4
A:203-217
B:203-217
C:203-217
D:203-217
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1pg8a_ (A:)
1b: SCOP_d1pg8b_ (B:)
1c: SCOP_d1pg8c_ (C:)
1d: SCOP_d1pg8d_ (D:)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
Cystathionine synthase-like
(64)
Protein domain
:
Methionine gamma-lyase, MGL
(14)
Pseudomonas putida [TaxId: 303]
(4)
1a
d1pg8a_
A:
1b
d1pg8b_
B:
1c
d1pg8c_
C:
1d
d1pg8d_
D:
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1pg8A01 (A:8-262)
1b: CATH_1pg8C01 (C:8-262)
1c: CATH_1pg8D01 (D:8-262)
1d: CATH_1pg8B01 (B:8-262)
2a: CATH_1pg8A02 (A:263-396)
2b: CATH_1pg8C02 (C:263-396)
2c: CATH_1pg8D02 (D:263-396)
2d: CATH_1pg8B02 (B:263-396)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Pseudomonas putida. Organism_taxid: 303
(3)
1a
1pg8A01
A:8-262
1b
1pg8C01
C:8-262
1c
1pg8D01
D:8-262
1d
1pg8B01
B:8-262
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Pseudomonas putida. Organism_taxid: 303
(3)
2a
1pg8A02
A:263-396
2b
1pg8C02
C:263-396
2c
1pg8D02
D:263-396
2d
1pg8B02
B:263-396
[
close CATH info
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cys_Met_Meta_PP_1pg8D01 (D:11-395)
1b: PFAM_Cys_Met_Meta_PP_1pg8D02 (D:11-395)
1c: PFAM_Cys_Met_Meta_PP_1pg8D03 (D:11-395)
1d: PFAM_Cys_Met_Meta_PP_1pg8D04 (D:11-395)
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Clan
:
PLP_aminotran
(240)
Family
:
Cys_Met_Meta_PP
(15)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(3)
1a
Cys_Met_Meta_PP-1pg8D01
D:11-395
1b
Cys_Met_Meta_PP-1pg8D02
D:11-395
1c
Cys_Met_Meta_PP-1pg8D03
D:11-395
1d
Cys_Met_Meta_PP-1pg8D04
D:11-395
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