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1QIP
Asym. Unit
Info
Asym.Unit (144 KB)
Biol.Unit 1 (71 KB)
Biol.Unit 2 (71 KB)
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(1)
Title
:
HUMAN GLYOXALASE I COMPLEXED WITH S-P-NITROBENZYLOXYCARBONYLGLUTATHIONE
Authors
:
A. D. Cameron, M. Ridderstrom, B. Olin, B. Mannervik
Date
:
14 Jun 99 (Deposition) - 24 Nov 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.72
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Lyase, Lactoylglutathione Lyase, Glyoxalase I
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. D. Cameron, M. Ridderstrom, B. Olin, M. J. Kavarana, D. J. Creighton B. Mannervik
Reaction Mechanism Of Glyoxalase I Explored By An X-Ray Crystallographic Analysis Of The Human Enzyme In Complex With A Transition State Analogue.
Biochemistry V. 38 13480 1999
[
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
1c: BETA-MERCAPTOETHANOL (BMEc)
1d: BETA-MERCAPTOETHANOL (BMEd)
2a: S-P-NITROBENZYLOXYCARBONYLGLUTATHI... (GNBa)
2b: S-P-NITROBENZYLOXYCARBONYLGLUTATHI... (GNBb)
2c: S-P-NITROBENZYLOXYCARBONYLGLUTATHI... (GNBc)
2d: S-P-NITROBENZYLOXYCARBONYLGLUTATHI... (GNBd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
4
Ligand/Ion
BETA-MERCAPTOETHANOL
2
GNB
4
Ligand/Ion
S-P-NITROBENZYLOXYCARBONYLGLUTATHIONE
3
ZN
4
Ligand/Ion
ZINC ION
[
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Sites
(24, 24)
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: GH1 (AUTHOR)
14: GH2 (AUTHOR)
15: GH3 (AUTHOR)
16: GH4 (AUTHOR)
17: HD2 (AUTHOR)
18: HD3 (AUTHOR)
19: HD4 (AUTHOR)
20: HD5 (AUTHOR)
21: ZN1 (AUTHOR)
22: ZN2 (AUTHOR)
23: ZN3 (AUTHOR)
24: ZN4 (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:126 , GLU A:172 , HOH A:1227 , HOH A:1228 , GLN B:33 , GLU B:99
BINDING SITE FOR RESIDUE ZN B 901
02
AC2
SOFTWARE
GLN A:33 , GLU A:99 , HOH A:1229 , HIS B:126 , GLU B:172 , HOH B:1225
BINDING SITE FOR RESIDUE ZN A 902
03
AC3
SOFTWARE
HIS C:126 , GLU C:172 , HOH C:1232 , GLN D:33 , GLU D:99 , HOH D:1227
BINDING SITE FOR RESIDUE ZN D 903
04
AC4
SOFTWARE
GLN C:33 , GLU C:99 , HOH C:1233 , HIS D:126 , GLU D:172 , HOH D:1228
BINDING SITE FOR RESIDUE ZN C 904
05
AC5
SOFTWARE
ARG A:122 , LEU A:160 , PHE A:162 , GLU A:172 , MET A:179 , LEU A:182 , HOH A:1227 , ARG B:37 , CYS B:60 , PHE B:67 , ILE B:88 , LEU B:92 , THR B:101 , ASN B:103 , BME B:204 , HOH B:1006 , HOH B:1040 , HOH B:1100 , HOH B:1102 , HOH B:1107 , HOH B:1113 , HOH B:1125 , HOH B:1129 , HOH B:1197 , SER C:17
BINDING SITE FOR RESIDUE GNB B 1001
06
AC6
SOFTWARE
ARG A:37 , GLN A:58 , CYS A:60 , PHE A:67 , PHE A:71 , ILE A:88 , LEU A:92 , THR A:101 , ASN A:103 , BME A:204 , HOH A:1037 , HOH A:1112 , HOH A:1138 , HOH A:1178 , ARG B:122 , MET B:157 , LEU B:160 , PHE B:162 , TRP B:170 , ASP D:154 , LYS D:158 , HOH D:1005
BINDING SITE FOR RESIDUE GNB A 1002
07
AC7
SOFTWARE
SER A:17 , HOH A:1116 , ARG C:122 , MET C:157 , LEU C:160 , PHE C:162 , MET C:179 , HOH C:1061 , ARG D:37 , CYS D:60 , PHE D:67 , ILE D:88 , LEU D:92 , THR D:101 , ASN D:103 , BME D:204 , HOH D:1049 , HOH D:1104 , HOH D:1105 , HOH D:1109 , HOH D:1114 , HOH D:1117 , HOH D:1125 , HOH D:1128 , HOH D:1194
BINDING SITE FOR RESIDUE GNB D 1003
08
AC8
SOFTWARE
ARG C:37 , CYS C:60 , PHE C:67 , ILE C:88 , LEU C:92 , THR C:101 , ASN C:103 , BME C:204 , HOH C:1005 , HOH C:1038 , HOH C:1092 , HOH C:1109 , HOH C:1113 , HOH C:1165 , HOH C:1171 , HOH C:1186 , HOH C:1225 , ARG D:122 , MET D:157 , LEU D:160 , PHE D:162 , MET D:179
BINDING SITE FOR RESIDUE GNB C 1004
09
AC9
SOFTWARE
GLN A:58 , LYS A:59 , CYS A:60 , PHE A:62 , GNB A:1002
BINDING SITE FOR RESIDUE BME A 204
10
BC1
SOFTWARE
GLN B:58 , LYS B:59 , CYS B:60 , LYS B:84 , GNB B:1001 , HOH B:1222
BINDING SITE FOR RESIDUE BME B 204
11
BC2
SOFTWARE
GLN C:58 , CYS C:60 , GNB C:1004
BINDING SITE FOR RESIDUE BME C 204
12
BC3
SOFTWARE
CYS D:60 , PHE D:62 , GNB D:1003
BINDING SITE FOR RESIDUE BME D 204
13
GH1
AUTHOR
ARG A:37 , ASN A:103 , ARG B:122
BINDING SITE FOR GSH MOIETY - SUBSTRATE BINDING SITE IS FORMED BY ZN2 HYD2 AND GSH2.
14
GH2
AUTHOR
ARG B:37 , ASN B:103 , ARG A:122
BINDING SITE FOR GSH MOIETY - SUBSTRATE BINDING SITE IS FORMED BY ZN1 HYD1 AND GSH1.
15
GH3
AUTHOR
ARG C:37 , ASN C:103 , ARG D:122
BINDING SITE FOR GSH MOIETY - SUBSTRATE BINDING SITE IS FORMED BY ZN2 HYD2 AND GSH2.
16
GH4
AUTHOR
ARG D:37 , ASN D:103 , ARG C:122
BINDING SITE FOR GSH MOIETY - SUBSTRATE BINDING SITE IS FORMED BY ZN1 HYD1 AND GSH1.
17
HD2
AUTHOR
CYS A:60 , PHE A:62 , MET A:65 , PHE A:67 , LEU A:69 , PHE A:71 , ILE A:88 , LEU A:92 , MET B:157 , LEU B:160 , PHE B:162 , LEU B:174 , MET B:179 , MET B:183
HYDROPHOBIC SUBSTRATE BINDING POCKET AT DIMER INTERFACE.
18
HD3
AUTHOR
CYS B:60 , PHE B:62 , MET B:65 , PHE B:67 , LEU B:69 , PHE B:71 , ILE B:88 , LEU B:92 , MET A:157 , LEU A:160 , PHE A:162 , LEU A:174 , MET A:179 , MET A:183
HYDROPHOBIC SUBSTRATE BINDING POCKET AT DIMER INTERFACE.
19
HD4
AUTHOR
CYS C:60 , PHE C:62 , MET C:65 , PHE C:67 , LEU C:69 , PHE C:71 , ILE C:88 , LEU C:92 , MET D:157 , LEU D:160 , PHE D:162 , LEU D:174 , MET D:179 , MET D:183
HYDROPHOBIC SUBSTRATE BINDING POCKET AT DIMER INTERFACE.
20
HD5
AUTHOR
CYS D:60 , PHE D:62 , MET D:65 , PHE D:67 , LEU D:69 , PHE D:71 , ILE D:88 , LEU D:92 , MET C:157 , LEU C:160 , PHE C:162 , LEU C:174 , MET C:179 , MET C:183
HYDROPHOBIC SUBSTRATE BINDING POCKET AT DIMER INTERFACE.
21
ZN1
AUTHOR
ZN A:902 , GLN A:33 , GLU A:99 , HIS B:126 , GLU B:172
ZINC BINDING SITE AT DIMER INTERFACE.
22
ZN2
AUTHOR
ZN B:901 , GLN B:33 , GLU B:99 , HIS A:126 , GLU A:172
ZINC BINDING SITE AT DIMER INTERFACE.
23
ZN3
AUTHOR
ZN C:904 , GLN C:33 , GLU C:99 , HIS D:126 , GLU D:172
ZINC BINDING SITE AT DIMER INTERFACE.
24
ZN4
AUTHOR
ZN D:903 , GLN D:33 , GLU D:99 , HIS C:126 , GLU C:172
ZINC BINDING SITE AT DIMER INTERFACE.
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_031078 (C18Y, chain A/B/C/D, )
2: VAR_013481 (E110A, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_031078
C
19
Y
LGUL_HUMAN
Polymorphism
17855424
A/B/C/D
C
18
Y
2
UniProt
VAR_013481
E
111
A
LGUL_HUMAN
Polymorphism
4746
A/B/C/D
E
110
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: VOC (A:30-176,B:30-176,C:30-176,D:30-17...)
2: GLYOXALASE_I_1 (A:33-54,B:33-54,C:33-54,D:33-54)
3: GLYOXALASE_I_2 (A:117-133,B:117-133,C:117-133,D:11...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
VOC
PS51819
Vicinal oxygen chelate (VOC) domain profile.
LGUL_HUMAN
31-177
4
A:30-176
B:30-176
C:30-176
D:30-176
2
GLYOXALASE_I_1
PS00934
Glyoxalase I signature 1.
LGUL_HUMAN
34-55
4
A:33-54
B:33-54
C:33-54
D:33-54
3
GLYOXALASE_I_2
PS00935
Glyoxalase I signature 2.
LGUL_HUMAN
118-134
4
A:117-133
B:117-133
C:117-133
D:117-133
[
close PROSITE info
]
Exons
(6, 24)
Info
All Exons
Exon 1.1 (A:8-27 | B:1-27 | C:8-27 | D:1-27)
Exon 1.2 (A:28-55 | B:28-55 | C:28-55 | D:28...)
Exon 1.3 (A:55-102 | B:55-102 | C:55-102 | D...)
Exon 1.4b (A:102-125 | B:102-125 | C:102-125 ...)
Exon 1.5 (A:125-155 | B:125-155 | C:125-155 ...)
Exon 1.6 (A:155-183 | B:155-183 | C:155-183 ...)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4b
5: Boundary 1.4b/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000373365
1
ENSE00001460407
chr6:
38670917-38670747
171
LGUL_HUMAN
1-28
28
4
A:8-27
B:1-27
C:8-27
D:1-27
20
27
20
27
1.2
ENST00000373365
2
ENSE00000750279
chr6:
38654750-38654668
83
LGUL_HUMAN
29-56
28
4
A:28-55
B:28-55
C:28-55
D:28-55
28
28
28
28
1.3
ENST00000373365
3
ENSE00000750268
chr6:
38652290-38652150
141
LGUL_HUMAN
56-103
48
4
A:55-102
B:55-102
C:55-102
D:55-102
48
48
48
48
1.4b
ENST00000373365
4b
ENSE00000750246
chr6:
38650651-38650584
68
LGUL_HUMAN
103-126
24
4
A:102-125
B:102-125
C:102-125
D:102-125
24
24
24
24
1.5
ENST00000373365
5
ENSE00002145874
chr6:
38649877-38649788
90
LGUL_HUMAN
126-156
31
4
A:125-155
B:125-155
C:125-155
D:125-155
31
31
31
31
1.6
ENST00000373365
6
ENSE00002199029
chr6:
38645159-38643719
1441
LGUL_HUMAN
156-184
29
4
A:155-183
B:155-183
C:155-183
D:155-183
29
29
29
29
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1qipa_ (A:)
1b: SCOP_d1qipb_ (B:)
1c: SCOP_d1qipc_ (C:)
1d: SCOP_d1qipd_ (D:)
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(
)
Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
(136)
Superfamily
:
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
(136)
Family
:
Glyoxalase I (lactoylglutathione lyase)
(16)
Protein domain
:
Glyoxalase I (lactoylglutathione lyase)
(10)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1qipa_
A:
1b
d1qipb_
B:
1c
d1qipc_
C:
1d
d1qipd_
D:
[
close SCOP info
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1qipA00 (A:8-183)
1b: CATH_1qipC00 (C:8-183)
1c: CATH_1qipB00 (B:1-183)
1d: CATH_1qipD00 (D:1-183)
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Homologous Superfamilies
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
(113)
Homologous Superfamily
:
2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1
(106)
Human (Homo sapiens)
(4)
1a
1qipA00
A:8-183
1b
1qipC00
C:8-183
1c
1qipB00
B:1-183
1d
1qipD00
D:1-183
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Glyoxalase_1qipD01 (D:30-173)
1b: PFAM_Glyoxalase_1qipD02 (D:30-173)
1c: PFAM_Glyoxalase_1qipD03 (D:30-173)
1d: PFAM_Glyoxalase_1qipD04 (D:30-173)
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Clan
:
Glyoxalase
(58)
Family
:
Glyoxalase
(34)
Homo sapiens (Human)
(2)
1a
Glyoxalase-1qipD01
D:30-173
1b
Glyoxalase-1qipD02
D:30-173
1c
Glyoxalase-1qipD03
D:30-173
1d
Glyoxalase-1qipD04
D:30-173
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