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3UBP
Biol. Unit 1
Info
Asym.Unit (147 KB)
Biol.Unit 1 (140 KB)
Biol.Unit 2 (411 KB)
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(1)
Title
:
DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE
Authors
:
S. Benini, W. R. Rypniewski, K. S. Wilson, S. Miletti, S. Mangani, S. Ciu
Date
:
16 Dec 98 (Deposition) - 17 Dec 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: A,B,C (3x)
Keywords
:
Urease, Bacillus Pasteurii, Nickel, Diamidophosphate, Metalloenzyme, Hydrolase
(Keyword Search:
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)
Reference
:
S. Benini, W. R. Rypniewski, K. S. Wilson, S. Miletti, S. Ciurli, S. Mangani
A New Proposal For Urease Mechanism Based On The Crystal Structures Of The Native And Inhibited Enzyme From Bacillus Pasteurii: Why Urea Hydrolysis Costs Two Nickels.
Structure Fold. Des. V. 7 205 1999
(for further references see the
PDB file header
)
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: DIAMIDOPHOSPHATE (2PAa)
2a: ACETYL GROUP (ACEa)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
4a: NICKEL (II) ION (NIa)
4b: NICKEL (II) ION (NIb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
2PA
1
Ligand/Ion
DIAMIDOPHOSPHATE
2
ACE
1
Mod. Amino Acid
ACETYL GROUP
3
KCX
1
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
NI
-1
Ligand/Ion
NICKEL (II) ION
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: CAT (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , 2PA C:902
BINDING SITE FOR RESIDUE NI C 900
2
AC2
SOFTWARE
HIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , 2PA C:902
BINDING SITE FOR RESIDUE NI C 901
3
AC3
SOFTWARE
HIS C:137 , HIS C:139 , ALA C:170 , KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , HIS C:323 , ASP C:363 , ALA C:366 , MET C:367 , NI C:900 , NI C:901
BINDING SITE FOR RESIDUE 2PA C 902
4
CAT
AUTHOR
HIS C:137 , HIS C:139 , KCX C:220 , HIS C:249 , HIS C:275 , ASP C:363
THE DINUCLEAR NICKEL 2+ METALLOCENTER IS INHIBITED BY A MOLECULE OF DIAMIDOPHOSPHATE, MIMICKING THE TETRAHEDRAL TRANSITION STATE OF UREA HYDROLYSIS
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: UREASE_1 (C:130-143)
2: UREASE_3 (C:132-570)
3: UREASE_2 (C:320-336)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UREASE_1
PS01120
Urease nickel ligands signature.
URE1_SPOPA
129-142
1
C:130-143
2
UREASE_3
PS51368
Urease domain profile.
URE1_SPOPA
131-569
1
C:132-570
3
UREASE_2
PS00145
Urease active site.
URE1_SPOPA
319-335
1
C:320-336
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d3ubpb_ (B:)
2a: SCOP_d3ubpc1 (C:1-131,C:435-483)
3a: SCOP_d3ubpa_ (A:)
4a: SCOP_d3ubpc2 (C:132-434,C:484-570)
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-clip
(280)
Superfamily
:
Urease, beta-subunit
(40)
Family
:
Urease, beta-subunit
(40)
Protein domain
:
Urease, beta-subunit
(39)
Bacillus pasteurii [TaxId: 1474]
(6)
1a
d3ubpb_
B:
Fold
:
Composite domain of metallo-dependent hydrolases
(103)
Superfamily
:
Composite domain of metallo-dependent hydrolases
(103)
Family
:
alpha-Subunit of urease
(40)
Protein domain
:
alpha-Subunit of urease
(40)
Bacillus pasteurii [TaxId: 1474]
(7)
2a
d3ubpc1
C:1-131,C:435-483
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Urease, gamma-subunit
(42)
Superfamily
:
Urease, gamma-subunit
(42)
Family
:
Urease, gamma-subunit
(40)
Protein domain
:
Urease, gamma-subunit
(40)
Bacillus pasteurii [TaxId: 1474]
(7)
3a
d3ubpa_
A:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
alpha-subunit of urease, catalytic domain
(40)
Protein domain
:
alpha-subunit of urease, catalytic domain
(40)
Bacillus pasteurii [TaxId: 1474]
(7)
4a
d3ubpc2
C:132-434,C:484-570
[
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]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_3ubpA00 (A:1-100)
2a: CATH_3ubpC02 (C:132-425,C:484-569)
3a: CATH_3ubpB00 (B:5-126)
4a: CATH_3ubpC01 (C:1-131,C:426-483)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Urease; subunit A
(36)
Homologous Superfamily
:
Urease, subunit A
(36)
Sporosarcina pasteurii. Organism_taxid: 1474. Strain: dsm 33.
(3)
1a
3ubpA00
A:1-100
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Sporosarcina pasteurii. Organism_taxid: 1474. Strain: dsm 33.
(3)
2a
3ubpC02
C:132-425,C:484-569
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Urease, subunit B
(35)
Homologous Superfamily
:
Urease, subunit B
(35)
Sporosarcina pasteurii. Organism_taxid: 1474. Strain: dsm 33.
(3)
3a
3ubpB00
B:5-126
Architecture
:
Roll
(1513)
Topology
:
Urease, subunit C; domain 1
(95)
Homologous Superfamily
:
Urease, subunit C, domain 1
(95)
Sporosarcina pasteurii. Organism_taxid: 1474. Strain: dsm 33.
(3)
4a
3ubpC01
C:1-131,C:426-483
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Pfam Domains
(0, 0)
Info
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Chain C
Asymmetric Unit 1
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Asym.Unit (147 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
Biol.Unit 2 (411 KB)
Header - Biol.Unit 2
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