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1W5P
Asym. Unit
Info
Asym.Unit (129 KB)
Biol.Unit 1 (476 KB)
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(1)
Title
:
STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTATIONS A129C, D131C, D139C, P132E)
Authors
:
F. Frere, H. Reents, W. -D. Schubert, D. W. Heinz, D. Jahn
Date
:
09 Aug 04 (Deposition) - 19 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (4x)
Keywords
:
Synthase, Evolution, Metalloenzyme, Porphobilinogen Synthase, Pseudomonas Aeruginosa, Protein Engineering,
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Frere, H. Reents, W. -D. Schubert, D. W. Heinz, D. Jahn
Tracking The Evolution Of Porphobilinogen Synthase Metal Dependence In Vitro
J. Mol. Biol. V. 345 1059 2005
[
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Hetero Components
(7, 21)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
2a: FORMIC ACID (FMTa)
2b: FORMIC ACID (FMTb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
4a: POTASSIUM ION (Ka)
4b: POTASSIUM ION (Kb)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
2
FMT
2
Ligand/Ion
FORMIC ACID
3
GOL
6
Ligand/Ion
GLYCEROL
4
K
2
Ligand/Ion
POTASSIUM ION
5
MG
2
Ligand/Ion
MAGNESIUM ION
6
SO4
2
Ligand/Ion
SULFATE ION
7
ZN
2
Ligand/Ion
ZINC ION
[
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]
Sites
(21, 21)
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)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:26 , LEU A:27 , ASP B:36 , ASP B:37 , ASP B:319 , GOL B:1345
BINDING SITE FOR RESIDUE K A1341
02
AC2
SOFTWARE
GLU A:245 , HOH A:2171 , HOH A:2173 , HOH A:2210 , HOH A:2211 , HOH A:2212
BINDING SITE FOR RESIDUE MG A1342
03
AC3
SOFTWARE
ARG A:20 , ASN B:196
BINDING SITE FOR RESIDUE SO4 A1343
04
AC4
SOFTWARE
CYS A:129 , CYS A:131 , CYS A:139 , HOH A:2266
BINDING SITE FOR RESIDUE ZN A1345
05
AC5
SOFTWARE
ASP A:36 , ASP A:37 , ASP A:319 , ARG B:26 , LEU B:27 , GOL B:1343 , HOH B:2031
BINDING SITE FOR RESIDUE K B1340
06
AC6
SOFTWARE
GLU B:245 , HOH B:2179 , HOH B:2181 , HOH B:2212 , HOH B:2213 , HOH B:2214
BINDING SITE FOR RESIDUE MG B1341
07
AC7
SOFTWARE
ASN A:196 , ARG B:20 , HOH B:2259
BINDING SITE FOR RESIDUE SO4 B1342
08
AC8
SOFTWARE
CYS B:129 , CYS B:131 , CYS B:139 , HOH B:2265
BINDING SITE FOR RESIDUE ZN B1348
09
AC9
SOFTWARE
ILE A:80 , PRO A:81 , GLU A:121 , HOH A:2262 , ASP B:22 , PHE B:23 , ARG B:26
BINDING SITE FOR RESIDUE EDO A1337
10
BC1
SOFTWARE
ASP A:235 , PRO A:236 , ALA A:237 , ARG B:29 , HOH B:2035
BINDING SITE FOR RESIDUE EDO A1338
11
BC2
SOFTWARE
ARG A:271 , ASP A:274 , HOH A:2224 , ARG B:271 , ASP B:274 , HOH B:2227
BINDING SITE FOR RESIDUE EDO A1339
12
BC3
SOFTWARE
ASP A:22 , PHE A:23 , ARG A:26 , ILE B:80 , GLU B:121 , HOH B:2258
BINDING SITE FOR RESIDUE EDO B1337
13
BC4
SOFTWARE
ASP B:46 , ARG B:110
BINDING SITE FOR RESIDUE EDO B1338
14
BC5
SOFTWARE
TYR A:211 , PHE A:214 , TYR A:283 , VAL A:285 , SER A:286 , TYR A:324
BINDING SITE FOR RESIDUE FMT A1340
15
BC6
SOFTWARE
LEU A:40 , PRO A:41 , VAL A:42 , VAL A:60 , GLU A:61 , HOH A:2069 , HOH A:2070 , HOH A:2255 , HOH A:2264 , HOH A:2265
BINDING SITE FOR RESIDUE GOL A1344
16
BC7
SOFTWARE
TYR B:211 , PHE B:214 , VAL B:285 , SER B:286 , TYR B:324
BINDING SITE FOR RESIDUE FMT B1339
17
BC8
SOFTWARE
THR A:34 , ASP A:37 , LYS A:314 , HOH A:2046 , ARG B:29 , GLU B:30 , ASN B:31 , VAL B:32 , K B:1340 , HOH B:2261
BINDING SITE FOR RESIDUE GOL B1343
18
BC9
SOFTWARE
PRO B:41 , VAL B:42 , VAL B:60 , GLU B:61 , HOH B:2076 , HOH B:2077 , HOH B:2252 , HOH B:2262 , HOH B:2263
BINDING SITE FOR RESIDUE GOL B1344
19
CC1
SOFTWARE
ARG A:29 , GLU A:30 , ASN A:31 , K A:1341 , THR B:34 , ASP B:37 , LYS B:314
BINDING SITE FOR RESIDUE GOL B1345
20
CC2
SOFTWARE
ARG A:29 , ASP B:235 , PRO B:236 , HOH B:2264
BINDING SITE FOR RESIDUE GOL B1346
21
CC3
SOFTWARE
GLN B:138 , ASN B:228 , LYS B:229
BINDING SITE FOR RESIDUE GOL B1347
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: D_ALA_DEHYDRATASE (A:253-265,B:253-265)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
D_ALA_DEHYDRATASE
PS00169
Delta-aminolevulinic acid dehydratase active site.
HEM2_PSEAE
253-265
2
A:253-265
B:253-265
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Exons
(0, 0)
Info
All Exons
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1w5pa_ (A:)
1b: SCOP_d1w5pb_ (B:)
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Protein Domains
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(
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Organisms
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)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)
(36)
Protein domain
:
automated matches
(15)
Pseudomonas aeruginosa [TaxId: 208964]
(6)
1a
d1w5pa_
A:
1b
d1w5pb_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1w5pA00 (A:6-336)
1b: CATH_1w5pB00 (B:6-336)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: pao1.
(6)
1a
1w5pA00
A:6-336
1b
1w5pB00
B:6-336
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_ALAD_1w5pB01 (B:10-333)
1b: PFAM_ALAD_1w5pB02 (B:10-333)
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Clan
:
TIM_barrel
(694)
Family
:
ALAD
(17)
Pseudomonas aeruginosa
(7)
1a
ALAD-1w5pB01
B:10-333
1b
ALAD-1w5pB02
B:10-333
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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