Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3L21

The crystal structure of a dimeric mutant of dihydrodipicolinate synthase (DAPA, RV2753C) from Mycobacterium Tuberculosis - DHDPS-A204R

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
A	0009085	biological_process	lysine biosynthetic process
A	0009089	biological_process	lysine biosynthetic process via diaminopimelate
A	0016829	molecular_function	lyase activity
A	0019877	biological_process	diaminopimelate biosynthetic process
A	0044281	biological_process	small molecule metabolic process
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
B	0009085	biological_process	lysine biosynthetic process
B	0009089	biological_process	lysine biosynthetic process via diaminopimelate
B	0016829	molecular_function	lyase activity
B	0019877	biological_process	diaminopimelate biosynthetic process
B	0044281	biological_process	small molecule metabolic process
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
C	0009085	biological_process	lysine biosynthetic process
C	0009089	biological_process	lysine biosynthetic process via diaminopimelate
C	0016829	molecular_function	lyase activity
C	0019877	biological_process	diaminopimelate biosynthetic process
C	0044281	biological_process	small molecule metabolic process
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
D	0009085	biological_process	lysine biosynthetic process
D	0009089	biological_process	lysine biosynthetic process via diaminopimelate
D	0016829	molecular_function	lyase activity
D	0019877	biological_process	diaminopimelate biosynthetic process
D	0044281	biological_process	small molecule metabolic process
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
E	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
E	0009085	biological_process	lysine biosynthetic process
E	0009089	biological_process	lysine biosynthetic process via diaminopimelate
E	0016829	molecular_function	lyase activity
E	0019877	biological_process	diaminopimelate biosynthetic process
E	0044281	biological_process	small molecule metabolic process
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0005886	cellular_component	plasma membrane
F	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
F	0009085	biological_process	lysine biosynthetic process
F	0009089	biological_process	lysine biosynthetic process via diaminopimelate
F	0016829	molecular_function	lyase activity
F	0019877	biological_process	diaminopimelate biosynthetic process
F	0044281	biological_process	small molecule metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 A 302

Chain	Residue
A	TYR90
A	HOH331
A	HOH696
B	THR89
B	TYR90
B	HIS94
B	HOH382
B	HOH1881

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 303

Chain	Residue
A	ARG238
A	HOH405
A	HOH700
A	HOH722
A	HOH1008
A	ARG204

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 A 304

Chain	Residue
A	SER24
A	GLY25

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 305

Chain	Residue
A	ASP176
A	LEU177
A	HIS178
A	SER179
A	HOH861
A	HOH1898
B	ARG265
B	ILE286
B	HOH494

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 306

Chain	Residue
A	LEU74
A	GLY78
A	ASP79
A	HIS108
A	HOH380
A	HOH689
D	ASP233

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 307

Chain	Residue
A	ALA10
A	ARG82
D	SER231

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 308

Chain	Residue
A	ARG300
C	GLY147

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACT A 309

Chain	Residue
A	ASP287
A	ALA290
A	ARG294
A	HOH788
A	HOH1604
C	HOH311
D	ALA173
D	LYS174

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 310

Chain	Residue
A	PRO146
A	PRO152
A	LYS174
A	HOH959
B	ASP270
B	HOH810
B	HOH1678

site_id	BC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 311

Chain	Residue
A	SER52
A	GLY53
A	THR54
A	SER58
A	ALA87
A	GLY88
A	LEU111
A	VAL112
A	VAL113
B	TYR117

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE BME A 312

Chain	Residue
A	ARG36
A	HIS40
A	HOH1863
C	ALA175
C	ASP176
C	HOH1862

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 301

Chain	Residue
A	LEU254
A	GLY255
B	LYS119
B	PRO121
B	ACT307
B	HOH549

site_id	BC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 302

Chain	Residue
A	LYS119
B	ARG148
B	MET251
B	GLY255
B	GLY256
B	ACT308
B	HOH383

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 B 303

Chain	Residue
B	ARG82
B	HIS108

site_id	BC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL B 304

Chain	Residue
B	THR62
B	ASP63
B	GLY64
B	ALA175
B	ASP176
B	LEU177
B	HIS178
B	SER179
B	HOH1773
B	HOH1881

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 305

Chain	Residue
B	ARG97
B	HIS178
B	ARG204
B	MET205
B	GOL309
B	HOH394

site_id	BC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL B 306

Chain	Residue
B	SER28
B	LEU29
B	GLU65
B	GLU68
B	PRO146
B	LYS174
B	ALA175
B	HOH339
B	HOH642
B	HOH1236
B	HOH1806

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT B 307

Chain	Residue
B	PRO121
B	GLN122
B	SO4301
B	HOH886

site_id	CC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACT B 308

Chain	Residue
B	TYR143
B	ILE145
B	ARG148
B	KPI171
B	SO4302
B	HOH330
B	HOH770

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 309

Chain	Residue
B	ASP63
B	HIS178
B	ARG204
B	GOL305
B	HOH373
B	HOH392

site_id	CC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ACT B 310

Chain	Residue
B	ARG11

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT B 311

Chain	Residue
B	PHE6
B	PRO139
B	PRO165
B	ASN166
B	HOH1245

site_id	CC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GOL B 312

Chain	Residue
B	ALA104
B	GLU105
B	LEU200
B	ARG204
B	ILE234
B	ARG238
B	ASN241
B	HOH376
B	HOH391
B	HOH392
B	HOH393
B	HOH830

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PYR B 313

Chain	Residue
B	ALA207
B	THR208
B	LEU226
B	PHE229
B	HOH1651

site_id	CC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL B 314

Chain	Residue
A	TYR117
B	SER52
B	GLY53
B	THR54
B	SER58
B	GLY86
B	ALA87
B	GLY88
B	LEU111
B	VAL112
B	VAL113

site_id	CC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE SO4 C 301

Chain	Residue
C	THR54
C	ARG148
C	GLY255
C	GLY256
C	VAL257
C	GOL304
C	HOH317
C	HOH329
C	HOH435
C	HOH496
C	HOH1877
D	SER118
D	LYS119

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 302

Chain	Residue
C	LEU200
C	PRO201
C	ARG204
C	ARG238

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 303

Chain	Residue
C	ARG82
C	HIS108
C	HOH674

site_id	DC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 304

Chain	Residue
C	ARG253
C	GLY255
C	SO4301
C	HOH1829
D	LYS119
D	PRO121
D	HOH753

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 305

Chain	Residue
C	LYS119
C	HOH311
C	HOH1820
D	GLY147
D	HOH325

site_id	DC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL C 306

Chain	Residue
A	ARG80
C	HIS178

site_id	DC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL C 307

Chain	Residue
C	ARG253
C	GLN285
C	HOH382

site_id	DC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT C 308

Chain	Residue
C	PRO121
C	GLN122
C	ARG123
C	HOH1891

site_id	DC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 309

Chain	Residue
C	SER52
C	GLY53
C	THR54
C	SER58
C	GLY88
C	LEU111
C	VAL112
C	VAL113
D	TYR117

site_id	DC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 D 301

Chain	Residue
C	THR89
C	HIS94
C	TYR116
C	HOH713
D	TYR90
D	HOH313
D	HOH1887

site_id	DC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 302

Chain	Residue
D	ARG82
D	HOH911
D	HOH1227

site_id	EC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL D 303

Chain	Residue
D	THR62
D	ASP63
D	GLY64

site_id	EC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL D 304

Chain	Residue
D	PRO121
D	GLN122
D	ARG123

site_id	EC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE GOL D 305

Chain	Residue
D	ALA243

site_id	EC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL D 306

Chain	Residue
C	TYR117
D	SER52
D	GLY53
D	THR54
D	SER58
D	GLY88
D	LEU111
D	VAL112
D	VAL113
D	HOH347

site_id	EC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL D 308

Chain	Residue
D	ARG253

site_id	EC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 301

Chain	Residue
E	ARG204
E	ILE234
E	ARG238
E	HOH834
E	HOH1443

site_id	EC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 302

Chain	Residue
A	ARG238
E	ARG253
E	HOH335
E	HOH775
E	HOH1671

site_id	EC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 303

Chain	Residue
E	ARG82
E	HIS108
E	HOH617

site_id	EC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL E 304

Chain	Residue
E	ASP195
E	ALA197
E	CME248
E	MET251
E	SER252
E	HOH1315

site_id	FC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT E 305

Chain	Residue
A	ARG204
E	ARG238
E	ILE242

site_id	FC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACT E 306

Chain	Residue
E	TYR90
F	THR89
F	HIS94
F	TYR116
F	ACT303
F	HOH579

site_id	FC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL E 307

Chain	Residue
E	ASP176
E	LEU177
E	HIS178
E	SER179

site_id	FC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL E 308

Chain	Residue
E	SER52
E	GLY53
E	THR54
E	SER58
E	GLY86
E	ALA87
E	GLY88
E	LEU111
E	VAL112
E	VAL113
F	TYR117

site_id	FC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL E 309

Chain	Residue
E	ARG238

site_id	FC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 F 301

Chain	Residue
F	ASP176
F	LEU177
F	HIS178
F	SER179
F	HOH801
F	HOH1050
F	HOH1243

site_id	FC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 F 302

Chain	Residue
F	ARG82
F	HIS108
F	HOH1764

site_id	FC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT F 303

Chain	Residue
E	THR89
E	TYR90
E	ACT306
F	TYR90

site_id	FC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL F 304

Chain	Residue
F	PRO121
F	GLN122
F	ARG123
F	HOH1843
F	HOH1882
F	HOH1885

site_id	GC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL F 305

Chain	Residue
E	LEU254
F	LYS119
F	PRO121
F	GOL306
F	HOH396
F	HOH1021
F	HOH1119
F	HOH1384
F	HOH1696
F	HOH1885

site_id	GC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL F 306

Chain	Residue
F	LYS119
F	PRO120
F	PRO121
F	GLN122
F	VAL151
F	GOL305
F	HOH1843

site_id	GC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL F 307

Chain	Residue
E	TYR117
F	SER52
F	GLY53
F	THR54
F	SER58
F	GLY88
F	LEU111
F	VAL112
F	VAL113

Functional Information from PROSITE/UniProt

site_id	PS00665
Number of Residues	18
Details	DHDPS_1 Dihydrodipicolinate synthase signature 1. GLVvsGTTGESptttdgE

Chain	Residue	Details
A	GLY48-GLU65

site_id	PS00666
Number of Residues	31
Details	DHDPS_2 Dihydrodipicolinate synthase signature 2. YDIPgrSavpIepdtiralashpn.IvGVKDA

Chain	Residue	Details
A	TYR143-ALA173

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	ACT_SITE: Proton donor/acceptor => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	TYR143
B	TYR143
C	TYR143
D	TYR143
E	TYR143
F	TYR143

site_id	SWS_FT_FI2
Number of Residues	6
Details	ACT_SITE: Schiff-base intermediate with substrate => ECO:0000255\|HAMAP-Rule:MF_00418, ECO:0000269\|PubMed:21672512

Chain	Residue	Details
A	KPI171
B	KPI171
C	KPI171
D	KPI171
E	KPI171
F	KPI171

site_id	SWS_FT_FI3
Number of Residues	12
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	THR55
E	ILE211
F	THR55
F	ILE211
A	ILE211
B	THR55
B	ILE211
C	THR55
C	ILE211
D	THR55
D	ILE211
E	THR55

site_id	SWS_FT_FI4
Number of Residues	12
Details	SITE: Part of a proton relay during catalysis => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	THR54
E	TYR117
F	THR54
F	TYR117
A	TYR117
B	THR54
B	TYR117
C	THR54
C	TYR117
D	THR54
D	TYR117
E	THR54

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)