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1XXX
Asym. Unit
Info
Asym.Unit (381 KB)
Biol.Unit 1 (192 KB)
Biol.Unit 2 (186 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE (DAPA, RV2753C) FROM MYCOBACTERIUM TUBERCULOSIS
Authors
:
G. Kefala, S. Panjikar, R. Janowski, M. S. Weiss, Tb Structural Genom Consortium (Tbsgc)
Date
:
09 Nov 04 (Deposition) - 14 Feb 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.28
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)
Keywords
:
Dihydrodipicolinate Synthase, Dapa, Rv2753C, Mycobacterium Tuberculosis, Lysine Biosynthesis, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Kefala, G. L. Evans, M. D. Griffin, S. R. Devenish, F. G. Pearce, M. A. Perugini, J. A. Gerrard, M. S. Weiss, R. C. Dobson
Crystal Structure And Kinetic Study Of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis.
Biochem. J. V. 411 351 2008
[
close entry info
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
2a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
2b: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTb)
2c: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTc)
2d: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTd)
2e: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTe)
2f: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTf)
2g: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTg)
2h: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTh)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
8
Ligand/Ion
CHLORIDE ION
2
DTT
8
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
3
MG
8
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
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: 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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:162 , HIS A:164 , ILE A:167 , HOH A:3026 , HOH A:3080 , HOH A:3233
BINDING SITE FOR RESIDUE MG A 2001
02
AC2
SOFTWARE
ALA B:162 , HIS B:164 , ILE B:167 , HOH B:3072 , HOH B:3232
BINDING SITE FOR RESIDUE MG B 2002
03
AC3
SOFTWARE
ALA C:162 , HIS C:164 , ILE C:167 , HOH C:3160
BINDING SITE FOR RESIDUE MG C 2003
04
AC4
SOFTWARE
ALA D:162 , HIS D:164 , ILE D:167 , HOH D:3090
BINDING SITE FOR RESIDUE MG D 2004
05
AC5
SOFTWARE
ALA E:162 , HIS E:164 , ILE E:167 , HOH E:3038
BINDING SITE FOR RESIDUE MG E 2005
06
AC6
SOFTWARE
ALA F:162 , HIS F:164 , ILE F:167
BINDING SITE FOR RESIDUE MG F 2006
07
AC7
SOFTWARE
ALA G:162 , HIS G:164 , ILE G:167 , HOH G:3147 , HOH G:3226
BINDING SITE FOR RESIDUE MG G 2007
08
AC8
SOFTWARE
ALA H:162 , HIS H:164 , ILE H:167 , HOH H:3095 , HOH H:3184
BINDING SITE FOR RESIDUE MG H 2008
09
AC9
SOFTWARE
LYS A:174 , SER A:179 , HOH A:3122
BINDING SITE FOR RESIDUE CL A 2009
10
BC1
SOFTWARE
PRO B:155 , LYS B:174 , SER B:179 , ILE B:183 , HOH B:3168 , HOH B:3193
BINDING SITE FOR RESIDUE CL B 2010
11
BC2
SOFTWARE
LYS C:174 , SER C:179 , ILE C:183 , HOH C:3024
BINDING SITE FOR RESIDUE CL C 2011
12
BC3
SOFTWARE
LYS D:174 , SER D:179 , ILE D:183 , HOH D:3079
BINDING SITE FOR RESIDUE CL D 2012
13
BC4
SOFTWARE
PRO E:155 , LYS E:174 , SER E:179 , ILE E:183
BINDING SITE FOR RESIDUE CL E 2013
14
BC5
SOFTWARE
LYS F:174 , SER F:179 , ILE F:183 , HOH F:3032 , HOH F:3048
BINDING SITE FOR RESIDUE CL F 2014
15
BC6
SOFTWARE
LYS G:174 , SER G:179 , ILE G:183
BINDING SITE FOR RESIDUE CL G 2015
16
BC7
SOFTWARE
LYS H:174 , SER H:179 , ILE H:183
BINDING SITE FOR RESIDUE CL H 2016
17
BC8
SOFTWARE
ASP A:195 , ALA A:197 , CYS A:248 , MET A:251 , SER A:252 , HOH A:3144
BINDING SITE FOR RESIDUE DTT A 3001
18
BC9
SOFTWARE
ASP B:195 , ASP B:196 , ALA B:197 , CYS B:248 , SER B:252
BINDING SITE FOR RESIDUE DTT B 3002
19
CC1
SOFTWARE
ASP C:195 , ALA C:197 , CYS C:248 , MET C:251 , SER C:252
BINDING SITE FOR RESIDUE DTT C 3003
20
CC2
SOFTWARE
ASP D:195 , ASP D:196 , ALA D:197 , CYS D:248 , SER D:252
BINDING SITE FOR RESIDUE DTT D 3004
21
CC3
SOFTWARE
ASP E:195 , ASP E:196 , ALA E:197 , CYS E:248 , SER E:252
BINDING SITE FOR RESIDUE DTT E 3005
22
CC4
SOFTWARE
ASP F:195 , ALA F:197 , CYS F:248 , SER F:252
BINDING SITE FOR RESIDUE DTT F 3006
23
CC5
SOFTWARE
ASP G:195 , ALA G:197 , CYS G:248 , MET G:251 , SER G:252
BINDING SITE FOR RESIDUE DTT G 3007
24
CC6
SOFTWARE
ASP H:195 , ALA H:197 , CYS H:248 , MET H:251 , SER H:252 , HOH H:3085
BINDING SITE FOR RESIDUE DTT H 3008
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 16)
Info
All PROSITE Patterns/Profiles
1: DHDPS_1 (A:48-65,B:48-65,C:48-65,D:48-65,E:...)
2: DHDPS_2 (A:143-173,B:143-173,C:143-173,D:14...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DHDPS_1
PS00665
Dihydrodipicolinate synthase signature 1.
DAPA_MYCTO
48-65
8
A:48-65
B:48-65
C:48-65
D:48-65
E:48-65
F:48-65
G:48-65
H:48-65
DAPA_MYCTU
48-65
8
A:48-65
B:48-65
C:48-65
D:48-65
E:48-65
F:48-65
G:48-65
H:48-65
2
DHDPS_2
PS00666
Dihydrodipicolinate synthase signature 2.
DAPA_MYCTO
143-173
8
A:143-173
B:143-173
C:143-173
D:143-173
E:143-173
F:143-173
G:143-173
H:143-173
DAPA_MYCTU
143-173
8
A:143-173
B:143-173
C:143-173
D:143-173
E:143-173
F:143-173
G:143-173
H:143-173
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1xxxa1 (A:5-300)
1b: SCOP_d1xxxb_ (B:)
1c: SCOP_d1xxxc_ (C:)
1d: SCOP_d1xxxd_ (D:)
1e: SCOP_d1xxxe_ (E:)
1f: SCOP_d1xxxf_ (F:)
1g: SCOP_d1xxxg_ (G:)
1h: SCOP_d1xxxh_ (H:)
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Classes
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
Class I aldolase
(182)
Protein domain
:
Dihydrodipicolinate synthase
(30)
Mycobacterium tuberculosis [TaxId: 1773]
(1)
1a
d1xxxa1
A:5-300
1b
d1xxxb_
B:
1c
d1xxxc_
C:
1d
d1xxxd_
D:
1e
d1xxxe_
E:
1f
d1xxxf_
F:
1g
d1xxxg_
G:
1h
d1xxxh_
H:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1xxxB00 (B:6-300)
1b: CATH_1xxxD00 (D:6-300)
1c: CATH_1xxxE00 (E:6-300)
1d: CATH_1xxxG00 (G:6-300)
1e: CATH_1xxxA00 (A:5-300)
1f: CATH_1xxxC00 (C:5-300)
1g: CATH_1xxxF00 (F:5-300)
1h: CATH_1xxxH00 (H:5-300)
View:
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Classes
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Architectures
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Topologies
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(2)
1a
1xxxB00
B:6-300
1b
1xxxD00
D:6-300
1c
1xxxE00
E:6-300
1d
1xxxG00
G:6-300
1e
1xxxA00
A:5-300
1f
1xxxC00
C:5-300
1g
1xxxF00
F:5-300
1h
1xxxH00
H:5-300
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_DHDPS_1xxxH01 (H:11-297)
1b: PFAM_DHDPS_1xxxH02 (H:11-297)
1c: PFAM_DHDPS_1xxxH03 (H:11-297)
1d: PFAM_DHDPS_1xxxH04 (H:11-297)
1e: PFAM_DHDPS_1xxxH05 (H:11-297)
1f: PFAM_DHDPS_1xxxH06 (H:11-297)
1g: PFAM_DHDPS_1xxxH07 (H:11-297)
1h: PFAM_DHDPS_1xxxH08 (H:11-297)
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Clans
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)
(
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)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
DHDPS
(40)
Mycobacterium tuberculosis
(2)
1a
DHDPS-1xxxH01
H:11-297
1b
DHDPS-1xxxH02
H:11-297
1c
DHDPS-1xxxH03
H:11-297
1d
DHDPS-1xxxH04
H:11-297
1e
DHDPS-1xxxH05
H:11-297
1f
DHDPS-1xxxH06
H:11-297
1g
DHDPS-1xxxH07
H:11-297
1h
DHDPS-1xxxH08
H:11-297
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