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1XXX
Biol. Unit 2
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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
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Hetero Components
(1, 4)
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
-1
Ligand/Ion
CHLORIDE ION
2
DTT
4
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(12, 12)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC4 (SOFTWARE)
06: BC5 (SOFTWARE)
07: BC6 (SOFTWARE)
08: BC7 (SOFTWARE)
09: CC3 (SOFTWARE)
10: CC4 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
ALA E:162 , HIS E:164 , ILE E:167 , HOH E:3038
BINDING SITE FOR RESIDUE MG E 2005
02
AC6
SOFTWARE
ALA F:162 , HIS F:164 , ILE F:167
BINDING SITE FOR RESIDUE MG F 2006
03
AC7
SOFTWARE
ALA G:162 , HIS G:164 , ILE G:167 , HOH G:3147 , HOH G:3226
BINDING SITE FOR RESIDUE MG G 2007
04
AC8
SOFTWARE
ALA H:162 , HIS H:164 , ILE H:167 , HOH H:3095 , HOH H:3184
BINDING SITE FOR RESIDUE MG H 2008
05
BC4
SOFTWARE
PRO E:155 , LYS E:174 , SER E:179 , ILE E:183
BINDING SITE FOR RESIDUE CL E 2013
06
BC5
SOFTWARE
LYS F:174 , SER F:179 , ILE F:183 , HOH F:3032 , HOH F:3048
BINDING SITE FOR RESIDUE CL F 2014
07
BC6
SOFTWARE
LYS G:174 , SER G:179 , ILE G:183
BINDING SITE FOR RESIDUE CL G 2015
08
BC7
SOFTWARE
LYS H:174 , SER H:179 , ILE H:183
BINDING SITE FOR RESIDUE CL H 2016
09
CC3
SOFTWARE
ASP E:195 , ASP E:196 , ALA E:197 , CYS E:248 , SER E:252
BINDING SITE FOR RESIDUE DTT E 3005
10
CC4
SOFTWARE
ASP F:195 , ALA F:197 , CYS F:248 , SER F:252
BINDING SITE FOR RESIDUE DTT F 3006
11
CC5
SOFTWARE
ASP G:195 , ALA G:197 , CYS G:248 , MET G:251 , SER G:252
BINDING SITE FOR RESIDUE DTT G 3007
12
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
[
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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
(2, 16)
Info
All PROSITE Patterns/Profiles
1: DHDPS_1 (E:48-65,F:48-65,G:48-65,H:48-65)
2: DHDPS_2 (E:143-173,F:143-173,G:143-173,H:14...)
;
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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
4
-
-
-
-
E:48-65
F:48-65
G:48-65
H:48-65
DAPA_MYCTU
48-65
4
-
-
-
-
E:48-65
F:48-65
G:48-65
H:48-65
2
DHDPS_2
PS00666
Dihydrodipicolinate synthase signature 2.
DAPA_MYCTO
143-173
4
-
-
-
-
E:143-173
F:143-173
G:143-173
H:143-173
DAPA_MYCTU
143-173
4
-
-
-
-
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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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
(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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Protein Domains
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Organisms
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(
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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:
[
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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)
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Homologous Superfamilies
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(
)
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
[
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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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(
)
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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