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1NVM
Biol. Unit 2
Info
Asym.Unit (462 KB)
Biol.Unit 1 (233 KB)
Biol.Unit 2 (228 KB)
Biol.Unit 3 (453 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A BIFUNCTIONAL ALDOLASE-DEHYDROGENASE : SEQUESTERING A REACTIVE AND VOLATILE INTERMEDIATE
Authors
:
A. B. Manjasetty, J. Powlowski, A. Vrielink
Date
:
04 Feb 03 (Deposition) - 17 Jun 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: A,B,C,D,E,F,G,H (1x)
Keywords
:
Sequestered Tunnel, Substrate Channeling, Bifunctional Enzyme, Lyase- Oxidoreductase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. B. Manjasetty, J. Powlowski, A. Vrielink
Crystal Structure Of A Bifunctional Aldolase-Dehydrogenase: Sequestering A Reactive And Volatile Intermediate
Proc. Natl. Acad. Sci. Usa V. 100 6992 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 12)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
2e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
2f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
4a: OXALATE ION (OXLa)
4b: OXALATE ION (OXLb)
4c: OXALATE ION (OXLc)
4d: OXALATE ION (OXLd)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
5k: SULFATE ION (SO4k)
5l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
-1
Ligand/Ion
MANGANESE (II) ION
2
MPD
2
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
NAD
1
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4
OXL
2
Ligand/Ion
OXALATE ION
5
SO4
7
Ligand/Ion
SULFATE ION
[
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Sites
(16, 16)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC5 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC8 (SOFTWARE)
09: BC9 (SOFTWARE)
10: CC1 (SOFTWARE)
11: CC2 (SOFTWARE)
12: CC5 (SOFTWARE)
13: CC8 (SOFTWARE)
14: CC9 (SOFTWARE)
15: DC1 (SOFTWARE)
16: DC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
ASP E:18 , HIS E:200 , HIS E:202 , OXL E:3510 , HOH E:3624
BINDING SITE FOR RESIDUE MN E 3506
02
AC4
SOFTWARE
ASP G:18 , HIS G:200 , HIS G:202 , OXL G:3511 , HOH G:3679
BINDING SITE FOR RESIDUE MN G 3507
03
AC7
SOFTWARE
ARG E:17 , ASP E:18 , PHE E:139 , MET E:141 , SER E:171 , HIS E:200 , HIS E:202 , TYR E:291 , MN E:3506 , HOH E:3624 , HOH E:3661
BINDING SITE FOR RESIDUE OXL E 3510
04
AC8
SOFTWARE
ARG G:17 , ASP G:18 , PHE G:139 , MET G:141 , SER G:171 , HIS G:200 , TYR G:291 , MN G:3507 , HOH G:3637
BINDING SITE FOR RESIDUE OXL G 3511
05
BC5
SOFTWARE
THR E:28 , LEU E:29 , ARG E:66 , HIS E:67 , HOH E:3701
BINDING SITE FOR RESIDUE SO4 E 3517
06
BC6
SOFTWARE
TYR E:258 , HOH E:3889
BINDING SITE FOR RESIDUE SO4 E 3518
07
BC7
SOFTWARE
GLY F:13 , ASN F:14 , ILE F:15 , SER F:80 , HOH F:3532 , HOH F:3714 , HOH F:3755 , HOH F:3782
BINDING SITE FOR RESIDUE SO4 F 3519
08
BC8
SOFTWARE
THR G:28 , LEU G:29 , ARG G:66 , HIS G:67 , HOH G:3816
BINDING SITE FOR RESIDUE SO4 G 3520
09
BC9
SOFTWARE
TYR G:258
BINDING SITE FOR RESIDUE SO4 G 3521
10
CC1
SOFTWARE
LYS E:8 , HIS E:82 , HOH E:3638 , HOH E:3648
BINDING SITE FOR RESIDUE SO4 E 3522
11
CC2
SOFTWARE
GLN C:104 , SER F:82 , ALA F:83 , HIS F:84 , VAL F:85 , HOH F:3715 , HOH F:3828
BINDING SITE FOR RESIDUE SO4 F 3523
12
CC5
SOFTWARE
ILE H:10 , GLY H:11 , SER H:12 , GLY H:13 , ASN H:14 , ILE H:15 , ILE H:38 , ALA H:78 , THR H:79 , SER H:80 , ALA H:83 , LEU H:103 , THR H:104 , PRO H:105 , CYS H:132 , SER H:163 , GLY H:165 , PRO H:166 , GLY H:167 , THR H:168 , ASN H:171 , ASN H:290 , MET H:294 , HOH H:3504 , HOH H:3571 , HOH H:3588 , HOH H:3602 , HOH H:3648 , HOH H:3726 , HOH H:3771
BINDING SITE FOR RESIDUE NAD H 3503
13
CC8
SOFTWARE
ARG E:248 , LEU E:249 , ALA G:174 , SER G:176 , ASP G:179 , HOH G:3650 , HOH G:3760
BINDING SITE FOR RESIDUE MPD G 3526
14
CC9
SOFTWARE
ALA E:174 , SER E:176 , ASP E:179 , LEU G:249
BINDING SITE FOR RESIDUE MPD E 3527
15
DC1
SOFTWARE
GLU B:61 , LEU B:90 , GLN B:93 , HOH B:3626 , HOH B:3848 , ARG G:130
BINDING SITE FOR RESIDUE MPD B 3528
16
DC2
SOFTWARE
HOH B:3597 , ARG C:130 , ASN C:131 , ALA F:89 , LEU F:90 , GLN F:93
BINDING SITE FOR RESIDUE MPD C 3529
[
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PYR_CT (E:9-261,G:9-261)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PYR_CT
PS50991
Pyruvate carboxyltransferase domain.
HOA_PSEUF
9-261
2
-
-
E:9-261
G:9-261
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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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, 16)
Info
All SCOP Domains
1a: SCOP_d1nvma1 (A:291-341)
1b: SCOP_d1nvmc1 (C:291-339)
1c: SCOP_d1nvme1 (E:291-339)
1d: SCOP_d1nvmg1 (G:291-341)
2a: SCOP_d1nvmb2 (B:132-286)
2b: SCOP_d1nvmd2 (D:132-286)
2c: SCOP_d1nvmf2 (F:132-286)
2d: SCOP_d1nvmh2 (H:132-286)
3a: SCOP_d1nvmb1 (B:1-131,B:287-312)
3b: SCOP_d1nvmd1 (D:3-131,D:287-310)
3c: SCOP_d1nvmf1 (F:4-131,F:287-312)
3d: SCOP_d1nvmh1 (H:4-131,H:287-310)
4a: SCOP_d1nvma2 (A:2-290)
4b: SCOP_d1nvmc2 (C:3-290)
4c: SCOP_d1nvme2 (E:2-290)
4d: SCOP_d1nvmg2 (G:3-290)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
RuvA C-terminal domain-like
(106)
Superfamily
:
post-HMGL domain-like
(11)
Family
:
DmpG/LeuA communication domain-like
(2)
Protein domain
:
4-hydroxy-2-oxovalerate aldolase DmpG, communication domain
(1)
Pseudomonas sp. [TaxId: 306]
(1)
1a
d1nvma1
A:291-341
1b
d1nvmc1
C:291-339
1c
d1nvme1
E:291-339
1d
d1nvmg1
G:291-341
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
GAPDH-like
(99)
Protein domain
:
Acetaldehyde dehydrogenase (acylating)
(1)
Pseudomonas sp. [TaxId: 306]
(1)
2a
d1nvmb2
B:132-286
2b
d1nvmd2
D:132-286
2c
d1nvmf2
F:132-286
2d
d1nvmh2
H:132-286
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Acetaldehyde dehydrogenase (acylating)
(1)
Pseudomonas sp. [TaxId: 306]
(1)
3a
d1nvmb1
B:1-131,B:287-312
3b
d1nvmd1
D:3-131,D:287-310
3c
d1nvmf1
F:4-131,F:287-312
3d
d1nvmh1
H:4-131,H:287-310
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
HMGL-like
(8)
Protein domain
:
4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain
(1)
Pseudomonas sp. [TaxId: 306]
(1)
4a
d1nvma2
A:2-290
4b
d1nvmc2
C:3-290
4c
d1nvme2
E:2-290
4d
d1nvmg2
G:3-290
[
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]
CATH Domains
(4, 16)
Info
all CATH domains
1a: CATH_1nvmB02 (B:132-285)
1b: CATH_1nvmD02 (D:132-285)
1c: CATH_1nvmF02 (F:132-285)
1d: CATH_1nvmH02 (H:132-285)
2a: CATH_1nvmB01 (B:1-131,B:286-312)
2b: CATH_1nvmF01 (F:4-131,F:286-312)
2c: CATH_1nvmD01 (D:3-131,D:286-310)
2d: CATH_1nvmH01 (H:4-131,H:286-310)
3a: CATH_1nvmA01 (A:2-271)
3b: CATH_1nvmE01 (E:2-271)
3c: CATH_1nvmC01 (C:3-271)
3d: CATH_1nvmG01 (G:3-271)
4a: CATH_1nvmA02 (A:278-341)
4b: CATH_1nvmG02 (G:278-341)
4c: CATH_1nvmC02 (C:278-339)
4d: CATH_1nvmE02 (E:278-339)
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)
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)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Cf600 (Pseudomonas sp)
(1)
1a
1nvmB02
B:132-285
1b
1nvmD02
D:132-285
1c
1nvmF02
F:132-285
1d
1nvmH02
H:132-285
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Cf600 (Pseudomonas sp)
(1)
2a
1nvmB01
B:1-131,B:286-312
2b
1nvmF01
F:4-131,F:286-312
2c
1nvmD01
D:3-131,D:286-310
2d
1nvmH01
H:4-131,H:286-310
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Cf600 (Pseudomonas sp)
(1)
3a
1nvmA01
A:2-271
3b
1nvmE01
E:2-271
3c
1nvmC01
C:3-271
3d
1nvmG01
G:3-271
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helicase, Ruva Protein; domain 3
(218)
Homologous Superfamily
:
[code=1.10.8.60, no name defined]
(73)
Cf600 (Pseudomonas sp)
(1)
4a
1nvmA02
A:278-341
4b
1nvmG02
G:278-341
4c
1nvmC02
C:278-339
4d
1nvmE02
E:278-339
[
close CATH info
]
Pfam Domains
(4, 16)
Info
all PFAM domains
1a: PFAM_Semialdhyde_dh_1nvmH01 (H:6-124)
1b: PFAM_Semialdhyde_dh_1nvmH02 (H:6-124)
1c: PFAM_Semialdhyde_dh_1nvmH03 (H:6-124)
1d: PFAM_Semialdhyde_dh_1nvmH04 (H:6-124)
2a: PFAM_HMGL_like_1nvmG01 (G:17-250)
2b: PFAM_HMGL_like_1nvmG02 (G:17-250)
2c: PFAM_HMGL_like_1nvmG03 (G:17-250)
2d: PFAM_HMGL_like_1nvmG04 (G:17-250)
3a: PFAM_AcetDehyd_dimer_1nvmH05 (H:132-285)
3b: PFAM_AcetDehyd_dimer_1nvmH06 (H:132-285)
3c: PFAM_AcetDehyd_dimer_1nvmH07 (H:132-285)
3d: PFAM_AcetDehyd_dimer_1nvmH08 (H:132-285)
4a: PFAM_DmpG_comm_1nvmG05 (G:274-339)
4b: PFAM_DmpG_comm_1nvmG06 (G:274-339)
4c: PFAM_DmpG_comm_1nvmG07 (G:274-339)
4d: PFAM_DmpG_comm_1nvmG08 (G:274-339)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Semialdhyde_dh
(22)
Pseudomonas sp. (strain CF600)
(1)
1a
Semialdhyde_dh-1nvmH01
H:6-124
1b
Semialdhyde_dh-1nvmH02
H:6-124
1c
Semialdhyde_dh-1nvmH03
H:6-124
1d
Semialdhyde_dh-1nvmH04
H:6-124
Clan
:
TIM_barrel
(694)
Family
:
HMGL-like
(13)
Pseudomonas sp. (strain CF600)
(1)
2a
HMGL-like-1nvmG01
G:17-250
2b
HMGL-like-1nvmG02
G:17-250
2c
HMGL-like-1nvmG03
G:17-250
2d
HMGL-like-1nvmG04
G:17-250
Clan
:
no clan defined [family: AcetDehyd-dimer]
(1)
Family
:
AcetDehyd-dimer
(1)
Pseudomonas sp. (strain CF600)
(1)
3a
AcetDehyd-dimer-1nvmH05
H:132-285
3b
AcetDehyd-dimer-1nvmH06
H:132-285
3c
AcetDehyd-dimer-1nvmH07
H:132-285
3d
AcetDehyd-dimer-1nvmH08
H:132-285
Clan
:
no clan defined [family: DmpG_comm]
(1)
Family
:
DmpG_comm
(1)
Pseudomonas sp. (strain CF600)
(1)
4a
DmpG_comm-1nvmG05
G:274-339
4b
DmpG_comm-1nvmG06
G:274-339
4c
DmpG_comm-1nvmG07
G:274-339
4d
DmpG_comm-1nvmG08
G:274-339
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