Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1VM6

Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0008652	biological_process	amino acid biosynthetic process
A	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
A	0009085	biological_process	lysine biosynthetic process
A	0009089	biological_process	lysine biosynthetic process via diaminopimelate
A	0016491	molecular_function	oxidoreductase activity
A	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
A	0019877	biological_process	diaminopimelate biosynthetic process
A	0050661	molecular_function	NADP binding
A	0051287	molecular_function	NAD binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0008652	biological_process	amino acid biosynthetic process
B	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
B	0009085	biological_process	lysine biosynthetic process
B	0009089	biological_process	lysine biosynthetic process via diaminopimelate
B	0016491	molecular_function	oxidoreductase activity
B	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
B	0019877	biological_process	diaminopimelate biosynthetic process
B	0050661	molecular_function	NADP binding
B	0051287	molecular_function	NAD binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0008652	biological_process	amino acid biosynthetic process
C	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
C	0009085	biological_process	lysine biosynthetic process
C	0009089	biological_process	lysine biosynthetic process via diaminopimelate
C	0016491	molecular_function	oxidoreductase activity
C	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
C	0019877	biological_process	diaminopimelate biosynthetic process
C	0050661	molecular_function	NADP binding
C	0051287	molecular_function	NAD binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0008652	biological_process	amino acid biosynthetic process
D	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
D	0009085	biological_process	lysine biosynthetic process
D	0009089	biological_process	lysine biosynthetic process via diaminopimelate
D	0016491	molecular_function	oxidoreductase activity
D	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
D	0019877	biological_process	diaminopimelate biosynthetic process
D	0050661	molecular_function	NADP binding
D	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT B 217

Chain	Residue
B	SER183
B	ARG184

site_id	AC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACT B 218

Chain	Residue
B	HOH342
B	HIS127
B	HIS128
B	LYS131
B	ACT222
B	NAD300
B	HOH315
B	HOH317

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT C 217

Chain	Residue
C	ASP43
C	GLY67
C	GLY200

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ACT B 219

Chain	Residue
B	GLU176

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACT A 217

Chain	Residue
A	HIS127
A	HIS128
A	LYS131
A	ACT218
A	NAD300
A	HOH318
A	HOH326
A	HOH392

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT B 220

Chain	Residue
B	SER110
B	LYS114
B	ALA145

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACT B 221

Chain	Residue
B	PHE98
B	ILE100
B	VAL186
B	GLY190
B	LYS193
C	HOH309

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT C 218

Chain	Residue
B	PHE108
B	LEU112
C	PHE108
C	GLU111

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT D 217

Chain	Residue
D	THR73
D	ASP133
D	NAD300
D	HOH321
D	HOH382

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACT A 218

Chain	Residue
A	THR73
A	TYR96
A	LYS131
A	SER136
A	GLY137
A	THR138
A	ACT217
A	NAD300

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACT D 218

Chain	Residue
D	THR73
D	TYR96
D	LYS131
D	SER136
D	GLY137
D	THR138

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACT B 222

Chain	Residue
B	THR73
B	TYR96
B	LYS131
B	SER136
B	GLY137
B	THR138
B	ACT218
B	NAD300

site_id	BC4
Number of Residues	25
Details	BINDING SITE FOR RESIDUE NAD A 300

Chain	Residue
A	GLY7
A	SER9
A	GLY10
A	ARG11
A	MET12
A	ASP32
A	VAL33
A	PHE48
A	SER49
A	SER50
A	ALA53
A	GLY71
A	THR73
A	ALA95
A	TYR96
A	ASN97
A	PHE98
A	LYS131
A	PHE187
A	ACT217
A	ACT218
A	HOH313
A	HOH314
A	HOH318
A	HOH326

site_id	BC5
Number of Residues	31
Details	BINDING SITE FOR RESIDUE NAD B 300

Chain	Residue
B	GLY71
B	THR73
B	ALA95
B	TYR96
B	ASN97
B	PHE98
B	LYS131
B	ASP133
B	PHE187
B	ACT218
B	ACT222
B	HOH307
B	HOH315
B	HOH316
B	HOH338
B	HOH342
B	HOH387
B	HOH435
B	HOH485
B	GLY7
B	SER9
B	GLY10
B	ARG11
B	MET12
B	ASP32
B	VAL33
B	PHE48
B	SER49
B	SER50
B	GLU52
B	ALA53

site_id	BC6
Number of Residues	24
Details	BINDING SITE FOR RESIDUE NAD C 300

Chain	Residue
C	GLY7
C	SER9
C	GLY10
C	ARG11
C	MET12
C	ASP32
C	VAL33
C	PHE48
C	SER49
C	SER50
C	GLU52
C	ALA53
C	GLY71
C	THR72
C	THR73
C	ALA95
C	TYR96
C	ASN97
C	PHE98
C	PHE187
C	PG4302
C	HOH337
C	HOH342
C	HOH384

site_id	BC7
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAD D 300

Chain	Residue
D	GLY7
D	SER9
D	GLY10
D	ARG11
D	MET12
D	ASP32
D	VAL33
D	PHE48
D	SER49
D	SER50
D	ALA53
D	GLY71
D	THR72
D	THR73
D	ALA95
D	TYR96
D	ASN97
D	PHE98
D	LYS131
D	ASP133
D	PHE187
D	ACT217
D	HOH319
D	HOH325
D	HOH331
D	HOH367
D	HOH395
D	HOH431

site_id	BC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO C 301

Chain	Residue
B	HIS-1
B	HIS-2
B	MET1
B	ASP43
B	HOH355
B	HOH436
C	ARG84
C	SER87
C	GLY204
C	MET205

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PG4 C 302

Chain	Residue
C	TYR96
C	PRO161
C	SER183
C	ARG184
C	NAD300
C	HOH326

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PG4 B 301

Chain	Residue
B	TYR8
B	GLN17
B	LYS30
B	GLU37
B	LEU39

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PG4 B 302

Chain	Residue
B	LEU75
B	LEU80
B	TYR96
B	HOH492
B	HOH493

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PG4 B 303

Chain	Residue
B	ARG107
B	PHE108
B	PHE213

Functional Information from PROSITE/UniProt

site_id	PS01298
Number of Residues	18
Details	DAPB Dihydrodipicolinate reductase signature. EIvEtHhrfKkDapSGTA

Chain	Residue	Details
A	GLU122-ALA139

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00102","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"18250105","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1VM6","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00102","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1arz

Chain	Residue	Details
A	LYS131
A	HIS127

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1arz

Chain	Residue	Details
B	LYS131
B	HIS127

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1arz

Chain	Residue	Details
C	LYS131
C	HIS127

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1arz

Chain	Residue	Details
D	LYS131
D	HIS127

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