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1XG3
Biol. Unit 1
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Asym.Unit (201 KB)
Biol.Unit 1 (196 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE C123S 2-METHYLISOCITRATE LYASE MUTANT FROM ESCHERICHIA COLI IN COMPLEX WITH THE REACTION PRODUCT, MG(II)-PYRUVATE AND SUCCINATE
Authors
:
S. Liu, Z. Lu, Y. Han, E. Melamud, D. Dunaway-Mariano, O. Herzberg
Date
:
16 Sep 04 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
2-Methylisocitrate Lyase/Product Complex, Succinate, Pyruvate, Isocitrate Lyase Superfamily
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Liu, Z. Lu, Y. Han, E. Melamud, D. Dunaway-Mariano, O. Herzberg
Crystal Structures Of 2-Methylisocitrate Lyase In Complex With Product And With Isocitrate Inhibitor Provide Insight Into Lyase Substrate Specificity, Catalysis And Evolution
Biochemistry V. 44 2949 2005
(for further references see the
PDB file header
)
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: PYRUVIC ACID (PYRa)
2b: PYRUVIC ACID (PYRb)
2c: PYRUVIC ACID (PYRc)
2d: PYRUVIC ACID (PYRd)
3a: SUCCINIC ACID (SINa)
3b: SUCCINIC ACID (SINb)
3c: SUCCINIC ACID (SINc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
PYR
4
Ligand/Ion
PYRUVIC ACID
3
SIN
3
Ligand/Ion
SUCCINIC ACID
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Sites
(11, 11)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:85 , PYR A:2105 , HOH A:2354 , HOH A:2355 , HOH A:2356
BINDING SITE FOR RESIDUE MG A 2101
02
AC2
SOFTWARE
ASP B:85 , PYR B:2205 , HOH B:2481 , HOH B:2482 , HOH B:2483
BINDING SITE FOR RESIDUE MG B 2201
03
AC3
SOFTWARE
ASP C:85 , PYR C:2305 , HOH C:2570 , HOH C:2571 , HOH C:2572
BINDING SITE FOR RESIDUE MG C 2301
04
AC4
SOFTWARE
ASP D:85 , PYR D:2405 , HOH D:2671 , HOH D:2672 , HOH D:2673
BINDING SITE FOR RESIDUE MG D 2401
05
AC5
SOFTWARE
TYR A:43 , SER A:45 , GLY A:46 , GLY A:47 , ASP A:85 , ARG A:158 , PRO A:236 , MG A:2101 , SIN A:2106 , HOH A:2354 , HOH A:2355
BINDING SITE FOR RESIDUE PYR A 2105
06
AC6
SOFTWARE
SER A:123 , GLY A:124 , HIS A:125 , ARG A:158 , GLU A:188 , ASN A:210 , THR A:212 , ARG A:241 , PYR A:2105 , HOH A:2210 , HOH A:2241 , HOH A:2355 , ARG B:270
BINDING SITE FOR RESIDUE SIN A 2106
07
AC7
SOFTWARE
TYR B:43 , SER B:45 , GLY B:46 , GLY B:47 , ASP B:85 , ARG B:158 , PRO B:236 , MG B:2201 , SIN B:2206 , HOH B:2481
BINDING SITE FOR RESIDUE PYR B 2205
08
AC8
SOFTWARE
ARG A:270 , SER B:123 , GLY B:124 , HIS B:125 , ARG B:158 , GLU B:188 , ASN B:210 , THR B:212 , ARG B:241 , PYR B:2205 , HOH B:2305 , HOH B:2482
BINDING SITE FOR RESIDUE SIN B 2206
09
AC9
SOFTWARE
TYR C:43 , SER C:45 , GLY C:46 , GLY C:47 , ASP C:85 , ARG C:158 , ASN C:210 , PRO C:236 , MG C:2301 , HOH C:2525
BINDING SITE FOR RESIDUE PYR C 2305
10
BC1
SOFTWARE
TYR D:43 , SER D:45 , GLY D:46 , GLY D:47 , ASP D:85 , ARG D:158 , PRO D:236 , MG D:2401 , SIN D:2406 , HOH D:2671 , HOH D:2672
BINDING SITE FOR RESIDUE PYR D 2405
11
BC2
SOFTWARE
ARG C:270 , SER D:123 , GLY D:124 , HIS D:125 , ARG D:158 , GLU D:188 , ASN D:210 , THR D:212 , ARG D:241 , PYR D:2405 , HOH D:2458 , HOH D:2509 , HOH D:2672
BINDING SITE FOR RESIDUE SIN D 2406
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ISOCITRATE_LYASE (A:121-126,B:121-126,C:121-126,D:12...)
;
View:
Select:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ISOCITRATE_LYASE
PS00161
Isocitrate lyase signature.
PRPB_ECOLI
121-126
4
A:121-126
B:121-126
C:121-126
D:121-126
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1xg3a_ (A:)
1b: SCOP_d1xg3b_ (B:)
1c: SCOP_d1xg3c_ (C:)
1d: SCOP_d1xg3d_ (D:)
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(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Phosphoenolpyruvate/pyruvate domain
(92)
Family
:
Phosphoenolpyruvate mutase/Isocitrate lyase-like
(20)
Protein domain
:
2-methylisocitrate lyase
(6)
Escherichia coli [TaxId: 562]
(4)
1a
d1xg3a_
A:
1b
d1xg3b_
B:
1c
d1xg3c_
C:
1d
d1xg3d_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1xg3D00 (D:3-285)
1b: CATH_1xg3B00 (B:3-288)
1c: CATH_1xg3C00 (C:3-289)
1d: CATH_1xg3A00 (A:2-289)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphoenolpyruvate-binding domains
(67)
Escherichia coli. Organism_taxid: 562.
(5)
1a
1xg3D00
D:3-285
1b
1xg3B00
B:3-288
1c
1xg3C00
C:3-289
1d
1xg3A00
A:2-289
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_PEP_mutase_1xg3D01 (D:10-255)
1b: PFAM_PEP_mutase_1xg3D02 (D:10-255)
1c: PFAM_PEP_mutase_1xg3D03 (D:10-255)
1d: PFAM_PEP_mutase_1xg3D04 (D:10-255)
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Clan
:
PK_TIM
(63)
Family
:
PEP_mutase
(13)
Escherichia coli (strain K12)
(4)
1a
PEP_mutase-1xg3D01
D:10-255
1b
PEP_mutase-1xg3D02
D:10-255
1c
PEP_mutase-1xg3D03
D:10-255
1d
PEP_mutase-1xg3D04
D:10-255
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Asymmetric Unit 1
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Asym.Unit (201 KB)
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