Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5US6

Structure of Dihydrodipicolinate Reductase from Vibrio vulnificus Bound to NADH and 2,6 Pyridine Dicarboxylic Acid with Intact Polyhistidine Tag

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
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0008652	biological_process	amino acid biosynthetic process
E	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
E	0009085	biological_process	lysine biosynthetic process
E	0009089	biological_process	lysine biosynthetic process via diaminopimelate
E	0016491	molecular_function	oxidoreductase activity
E	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
E	0019877	biological_process	diaminopimelate biosynthetic process
E	0050661	molecular_function	NADP binding
E	0051287	molecular_function	NAD binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0008652	biological_process	amino acid biosynthetic process
F	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
F	0009085	biological_process	lysine biosynthetic process
F	0009089	biological_process	lysine biosynthetic process via diaminopimelate
F	0016491	molecular_function	oxidoreductase activity
F	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
F	0019877	biological_process	diaminopimelate biosynthetic process
F	0050661	molecular_function	NADP binding
F	0051287	molecular_function	NAD binding
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0008652	biological_process	amino acid biosynthetic process
G	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
G	0009085	biological_process	lysine biosynthetic process
G	0009089	biological_process	lysine biosynthetic process via diaminopimelate
G	0016491	molecular_function	oxidoreductase activity
G	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
G	0019877	biological_process	diaminopimelate biosynthetic process
G	0050661	molecular_function	NADP binding
G	0051287	molecular_function	NAD binding
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0008652	biological_process	amino acid biosynthetic process
H	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
H	0009085	biological_process	lysine biosynthetic process
H	0009089	biological_process	lysine biosynthetic process via diaminopimelate
H	0016491	molecular_function	oxidoreductase activity
H	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
H	0019877	biological_process	diaminopimelate biosynthetic process
H	0050661	molecular_function	NADP binding
H	0051287	molecular_function	NAD binding
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0008652	biological_process	amino acid biosynthetic process
I	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
I	0009085	biological_process	lysine biosynthetic process
I	0009089	biological_process	lysine biosynthetic process via diaminopimelate
I	0016491	molecular_function	oxidoreductase activity
I	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
I	0019877	biological_process	diaminopimelate biosynthetic process
I	0050661	molecular_function	NADP binding
I	0051287	molecular_function	NAD binding
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0008652	biological_process	amino acid biosynthetic process
J	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
J	0009085	biological_process	lysine biosynthetic process
J	0009089	biological_process	lysine biosynthetic process via diaminopimelate
J	0016491	molecular_function	oxidoreductase activity
J	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
J	0019877	biological_process	diaminopimelate biosynthetic process
J	0050661	molecular_function	NADP binding
J	0051287	molecular_function	NAD binding
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0008652	biological_process	amino acid biosynthetic process
K	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
K	0009085	biological_process	lysine biosynthetic process
K	0009089	biological_process	lysine biosynthetic process via diaminopimelate
K	0016491	molecular_function	oxidoreductase activity
K	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
K	0019877	biological_process	diaminopimelate biosynthetic process
K	0050661	molecular_function	NADP binding
K	0051287	molecular_function	NAD binding
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0008652	biological_process	amino acid biosynthetic process
L	0008839	molecular_function	4-hydroxy-tetrahydrodipicolinate reductase
L	0009085	biological_process	lysine biosynthetic process
L	0009089	biological_process	lysine biosynthetic process via diaminopimelate
L	0016491	molecular_function	oxidoreductase activity
L	0016726	molecular_function	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
L	0019877	biological_process	diaminopimelate biosynthetic process
L	0050661	molecular_function	NADP binding
L	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	20
Details	binding site for residue NAD A 1001

Chain	Residue
A	GLY8
A	SER80
A	GLY98
A	THR100
A	ALA122
A	PRO123
A	ASN124
A	TYR125
A	LYS159
A	ASP161
A	PDC1002
A	GLY11
A	HOH1103
A	ARG12
A	MET13
A	SER33
A	GLU34
A	ARG35
A	PHE75
A	THR76

site_id	AC2
Number of Residues	9
Details	binding site for residue PDC A 1002

Chain	Residue
A	THR100
A	PRO123
A	HIS156
A	LYS159
A	SER164
A	GLY165
A	THR166
A	NAD1001
A	HOH1103

site_id	AC3
Number of Residues	2
Details	binding site for residue SO4 A 1003

Chain	Residue
A	ASN16
A	ARG236

site_id	AC4
Number of Residues	1
Details	binding site for residue SO4 A 1004

Chain	Residue
A	LYS138

site_id	AC5
Number of Residues	19
Details	binding site for residue NAD B 1001

Chain	Residue
B	GLY11
B	ARG12
B	MET13
B	SER33
B	GLU34
B	ARG35
B	PHE75
B	THR76
B	SER80
B	GLY98
B	THR100
B	ALA122
B	PRO123
B	ASN124
B	TYR125
B	LYS159
B	ASP161
B	PHE239
B	PDC1002

site_id	AC6
Number of Residues	8
Details	binding site for residue PDC B 1002

Chain	Residue
B	THR100
B	PRO123
B	HIS156
B	LYS159
B	SER164
B	GLY165
B	THR166
B	NAD1001

site_id	AC7
Number of Residues	2
Details	binding site for residue SO4 B 1003

Chain	Residue
B	ASN16
B	ARG236

site_id	AC8
Number of Residues	19
Details	binding site for residue NAD C 1001

Chain	Residue
C	GLY11
C	ARG12
C	MET13
C	SER33
C	GLU34
C	ARG35
C	PHE75
C	THR76
C	SER80
C	GLY98
C	THR100
C	ALA122
C	PRO123
C	ASN124
C	TYR125
C	LYS159
C	PDC1002
C	HOH1103
C	HOH1104

site_id	AC9
Number of Residues	9
Details	binding site for residue PDC C 1002

Chain	Residue
C	THR100
C	PRO123
C	HIS156
C	LYS159
C	SER164
C	GLY165
C	THR166
C	NAD1001
C	HOH1103

site_id	AD1
Number of Residues	3
Details	binding site for residue SO4 C 1003

Chain	Residue
C	ARG12
C	ASN16
C	ARG236

site_id	AD2
Number of Residues	4
Details	binding site for residue SO4 D 301

Chain	Residue
D	LYS159
D	GLY165
D	THR166
D	SO4302

site_id	AD3
Number of Residues	3
Details	binding site for residue SO4 D 302

Chain	Residue
D	HIS156
D	LYS159
D	SO4301

site_id	AD4
Number of Residues	1
Details	binding site for residue SO4 D 303

Chain	Residue
D	LYS138

site_id	AD5
Number of Residues	1
Details	binding site for residue SO4 D 304

Chain	Residue
D	ARG3

site_id	AD6
Number of Residues	20
Details	binding site for residue NAD E 1001

Chain	Residue
E	GLY8
E	GLY11
E	ARG12
E	MET13
E	SER33
E	GLU34
E	ARG35
E	PHE75
E	THR76
E	SER80
E	GLY98
E	THR100
E	ALA122
E	PRO123
E	ASN124
E	TYR125
E	LYS159
E	ASP161
E	PDC1002
E	HOH1108

site_id	AD7
Number of Residues	10
Details	binding site for residue PDC E 1002

Chain	Residue
E	THR100
E	PRO123
E	HIS156
E	LYS159
E	SER164
E	GLY165
E	THR166
E	NAD1001
E	HOH1104
E	HOH1108

site_id	AD8
Number of Residues	2
Details	binding site for residue SO4 E 1003

Chain	Residue
E	ASN16
E	ARG236

site_id	AD9
Number of Residues	2
Details	binding site for residue SO4 E 1004

Chain	Residue
E	LYS138
F	LYS138

site_id	AE1
Number of Residues	18
Details	binding site for residue NAD F 1001

Chain	Residue
F	GLY8
F	GLY11
F	ARG12
F	MET13
F	SER33
F	GLU34
F	ARG35
F	PHE75
F	THR76
F	SER80
F	GLY98
F	THR100
F	ALA122
F	PRO123
F	ASN124
F	TYR125
F	LYS159
F	PDC1002

site_id	AE2
Number of Residues	8
Details	binding site for residue PDC F 1002

Chain	Residue
F	THR100
F	PRO123
F	HIS156
F	LYS159
F	SER164
F	GLY165
F	THR166
F	NAD1001

site_id	AE3
Number of Residues	2
Details	binding site for residue SO4 F 1003

Chain	Residue
F	ASN16
F	ARG236

site_id	AE4
Number of Residues	20
Details	binding site for residue NAD G 1001

Chain	Residue
G	GLY8
G	GLY11
G	ARG12
G	MET13
G	SER33
G	GLU34
G	ARG35
G	PHE75
G	THR76
G	SER80
G	GLY98
G	THR100
G	ALA122
G	PRO123
G	ASN124
G	TYR125
G	LYS159
G	PDC1002
G	HOH1102
G	HOH1103

site_id	AE5
Number of Residues	10
Details	binding site for residue PDC G 1002

Chain	Residue
G	THR100
G	PRO123
G	HIS156
G	LYS159
G	SER164
G	GLY165
G	THR166
G	NAD1001
G	HOH1102
G	HOH1103

site_id	AE6
Number of Residues	3
Details	binding site for residue SO4 G 1003

Chain	Residue
G	ASN16
G	ARG236
G	HOH1105

site_id	AE7
Number of Residues	2
Details	binding site for residue SO4 H 301

Chain	Residue
H	THR103
H	GLU104

site_id	AE8
Number of Residues	6
Details	binding site for residue SO4 H 302

Chain	Residue
H	LYS159
H	ASP161
H	SER164
H	GLY165
H	THR166
H	SO4303

site_id	AE9
Number of Residues	4
Details	binding site for residue SO4 H 303

Chain	Residue
H	HIS156
H	LYS159
H	ARG236
H	SO4302

site_id	AF1
Number of Residues	3
Details	binding site for residue SO4 H 304

Chain	Residue
H	GLN90
H	TYR91
H	GLY92

site_id	AF2
Number of Residues	1
Details	binding site for residue SO4 H 305

Chain	Residue
H	LYS138

site_id	AF3
Number of Residues	9
Details	binding site for residue PDC I 301

Chain	Residue
I	THR100
I	PRO123
I	HIS156
I	LYS159
I	SER164
I	GLY165
I	THR166
I	NAD302
I	HOH404

site_id	AF4
Number of Residues	19
Details	binding site for residue NAD I 302

Chain	Residue
I	GLY8
I	GLY11
I	ARG12
I	MET13
I	SER33
I	GLU34
I	ARG35
I	PHE75
I	THR76
I	SER80
I	GLY98
I	THR100
I	ALA122
I	PRO123
I	ASN124
I	TYR125
I	LYS159
I	ASP161
I	PDC301

site_id	AF5
Number of Residues	3
Details	binding site for residue SO4 I 303

Chain	Residue
I	ARG12
I	ASN16
I	ARG236

site_id	AF6
Number of Residues	1
Details	binding site for residue SO4 I 304

Chain	Residue
I	LYS138

site_id	AF7
Number of Residues	20
Details	binding site for residue NAD J 1001

Chain	Residue
J	GLY8
J	GLY11
J	ARG12
J	MET13
J	SER33
J	GLU34
J	ARG35
J	PHE75
J	THR76
J	SER80
J	GLY98
J	THR100
J	ALA122
J	PRO123
J	ASN124
J	TYR125
J	LYS159
J	ASP161
J	PDC1002
J	HOH1105

site_id	AF8
Number of Residues	8
Details	binding site for residue PDC J 1002

Chain	Residue
J	THR100
J	PRO123
J	HIS156
J	LYS159
J	SER164
J	GLY165
J	THR166
J	NAD1001

site_id	AF9
Number of Residues	2
Details	binding site for residue SO4 J 1003

Chain	Residue
J	ASN16
J	ARG236

site_id	AG1
Number of Residues	22
Details	binding site for residue NAD K 1001

Chain	Residue
K	GLY8
K	GLY11
K	ARG12
K	MET13
K	SER33
K	GLU34
K	ARG35
K	PHE75
K	THR76
K	SER80
K	GLY98
K	THR100
K	ALA122
K	PRO123
K	ASN124
K	TYR125
K	LYS159
K	PHE239
K	PDC1002
K	HOH1102
K	HOH1104
K	HOH1106

site_id	AG2
Number of Residues	8
Details	binding site for residue PDC K 1002

Chain	Residue
K	THR100
K	PRO123
K	HIS156
K	LYS159
K	GLY165
K	THR166
K	NAD1001
K	HOH1104

site_id	AG3
Number of Residues	2
Details	binding site for residue SO4 K 1003

Chain	Residue
K	ASN16
K	ARG236

site_id	AG4
Number of Residues	1
Details	binding site for residue SO4 K 1004

Chain	Residue
K	ARG15

site_id	AG5
Number of Residues	5
Details	binding site for residue SO4 L 301

Chain	Residue
L	LYS159
L	ASP161
L	SER164
L	GLY165
L	THR166

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	GLU150-ALA167

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
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	12
Details	Active site: {"description":"Proton donor","evidences":[{"source":"HAMAP-Rule","id":"MF_00102","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	166
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00102","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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