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1UKJ
Asym. Unit
Info
Asym.Unit (272 KB)
Biol.Unit 1 (266 KB)
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(1)
Title
:
DETAILED STRUCTURE OF L-METHIONINE-LYASE FROM PSEUDOMONAS PUTIDA
Authors
:
S. Misaki, A. Takimoto, T. Takakura, T. Yoshioka, M. Yamashita, T. Tamura, H. Tanaka, K. Inagaki
Date
:
24 Aug 03 (Deposition) - 19 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Pyridoxal Phosphate, Pseudomonas Putida, Methionine, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Misaki, A. Takimoto, T. Takakura, T. Yoshioka, M. Yamashita, T. Tamura, H. Tanaka, K. Inagaki
Detailed Structure Of L-Methionine -Lyase From Pseudomonas Putida
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(2, 9)
Info
All Hetero Components
1a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
1b: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPb)
1c: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPc)
1d: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
View:
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Label:
No.
Name
Count
Type
Full Name
1
LLP
4
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2
SO4
5
Ligand/Ion
SULFATE ION
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:114 , VAL A:339 , SER A:340 , GLN A:349 , ARG A:375 , HOH A:2671 , HOH A:3090
BINDING SITE FOR RESIDUE SO4 A 400
2
AC2
SOFTWARE
TYR B:614 , VAL B:839 , SER B:840 , GLN B:849 , ARG B:875 , HOH B:2121 , HOH B:2644
BINDING SITE FOR RESIDUE SO4 B 900
3
AC3
SOFTWARE
TYR C:1114 , VAL C:1339 , SER C:1340 , LEU C:1341 , GLN C:1349 , ARG C:1375 , HOH C:2253 , HOH C:2432
BINDING SITE FOR RESIDUE SO4 C 1400
4
AC4
SOFTWARE
TYR D:1614 , LLP D:1711 , VAL D:1839 , SER D:1840 , GLN D:1849 , ARG D:1875 , HOH D:2167 , HOH D:3037
BINDING SITE FOR RESIDUE SO4 D 1900
5
AC5
SOFTWARE
VAL B:532 , HIS B:750 , HOH B:2244 , HOH B:2425 , GLN C:1034 , HIS D:1750
BINDING SITE FOR RESIDUE SO4 B 1901
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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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: CYS_MET_METAB_PP (A:203-217,B:703-717,C:1203-1217,D:...)
;
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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:703-717
C:1203-1217
D:1703-1717
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Exons
(0, 0)
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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_d1ukja_ (A:)
1b: SCOP_d1ukjb_ (B:)
1c: SCOP_d1ukjc_ (C:)
1d: SCOP_d1ukjd_ (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
d1ukja_
A:
1b
d1ukjb_
B:
1c
d1ukjc_
C:
1d
d1ukjd_
D:
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ukjA01 (A:8-262)
1b: CATH_1ukjB01 (B:508-762)
1c: CATH_1ukjC01 (C:1008-1262)
1d: CATH_1ukjD01 (D:1508-1762)
2a: CATH_1ukjA02 (A:263-396)
2b: CATH_1ukjB02 (B:763-896)
2c: CATH_1ukjC02 (C:1263-1396)
2d: CATH_1ukjD02 (D:1763-1896)
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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.
(1)
1a
1ukjA01
A:8-262
1b
1ukjB01
B:508-762
1c
1ukjC01
C:1008-1262
1d
1ukjD01
D:1508-1762
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Pseudomonas putida. Organism_taxid: 303.
(1)
2a
1ukjA02
A:263-396
2b
1ukjB02
B:763-896
2c
1ukjC02
C:1263-1396
2d
1ukjD02
D:1763-1896
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cys_Met_Meta_PP_1ukjD01 (D:1511-1895)
1b: PFAM_Cys_Met_Meta_PP_1ukjD02 (D:1511-1895)
1c: PFAM_Cys_Met_Meta_PP_1ukjD03 (D:1511-1895)
1d: PFAM_Cys_Met_Meta_PP_1ukjD04 (D:1511-1895)
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Clan
:
PLP_aminotran
(240)
Family
:
Cys_Met_Meta_PP
(15)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(3)
1a
Cys_Met_Meta_PP-1ukjD01
D:1511-1895
1b
Cys_Met_Meta_PP-1ukjD02
D:1511-1895
1c
Cys_Met_Meta_PP-1ukjD03
D:1511-1895
1d
Cys_Met_Meta_PP-1ukjD04
D:1511-1895
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Asym.Unit (272 KB)
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