Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1YL7

the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)

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	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	0009274	cellular_component	peptidoglycan-based cell wall
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
A	0070402	molecular_function	NADPH binding
A	0070404	molecular_function	NADH binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
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	0009274	cellular_component	peptidoglycan-based cell wall
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
B	0070402	molecular_function	NADPH binding
B	0070404	molecular_function	NADH binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
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	0009274	cellular_component	peptidoglycan-based cell wall
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
C	0070402	molecular_function	NADPH binding
C	0070404	molecular_function	NADH binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
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	0009274	cellular_component	peptidoglycan-based cell wall
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
D	0070402	molecular_function	NADPH binding
D	0070404	molecular_function	NADH binding
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
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	0009274	cellular_component	peptidoglycan-based cell wall
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
E	0070402	molecular_function	NADPH binding
E	0070404	molecular_function	NADH binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0005886	cellular_component	plasma membrane
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	0009274	cellular_component	peptidoglycan-based cell wall
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
F	0070402	molecular_function	NADPH binding
F	0070404	molecular_function	NADH binding
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0005886	cellular_component	plasma membrane
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	0009274	cellular_component	peptidoglycan-based cell wall
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
G	0070402	molecular_function	NADPH binding
G	0070404	molecular_function	NADH binding
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0005886	cellular_component	plasma membrane
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	0009274	cellular_component	peptidoglycan-based cell wall
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
H	0070402	molecular_function	NADPH binding
H	0070404	molecular_function	NADH binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 401

Chain	Residue
D	VAL20
D	ALA21
D	ALA23
D	LEU26
D	HOH505
D	HOH585

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG G 402

Chain	Residue
G	LEU26
G	HOH511
G	VAL20
G	ALA21
G	ALA23

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG E 403

Chain	Residue
E	VAL20
E	ALA21
E	ALA23
E	LEU26

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 404

Chain	Residue
B	VAL20
B	ALA21
B	ALA23
B	LEU26
B	HOH555

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 405

Chain	Residue
A	VAL20
A	ALA21
A	ALA23
A	LEU26

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG F 406

Chain	Residue
F	VAL20
F	ALA21
F	ALA23
F	LEU26

site_id	AC7
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NAI A 501

Chain	Residue
A	GLY7
A	LYS9
A	GLY10
A	LYS11
A	VAL12
A	LEU32
A	ASP33
A	ALA34
A	PHE52
A	THR53
A	VAL57
A	GLY75
A	THR76
A	THR77
A	ALA102
A	PRO103
A	ASN104
A	PHE105
A	PHE217
A	HOH503
A	HOH512

site_id	AC8
Number of Residues	20
Details	BINDING SITE FOR RESIDUE NAI B 502

Chain	Residue
B	GLY7
B	LYS9
B	GLY10
B	LYS11
B	VAL12
B	LEU32
B	ASP33
B	ALA34
B	PHE52
B	THR53
B	VAL57
B	GLY75
B	THR76
B	THR77
B	ALA102
B	PRO103
B	ASN104
B	PHE105
B	PHE217
B	HOH516

site_id	AC9
Number of Residues	18
Details	BINDING SITE FOR RESIDUE NAI C 503

Chain	Residue
C	GLY7
C	LYS9
C	GLY10
C	LYS11
C	VAL12
C	ASP33
C	ALA34
C	PHE52
C	THR53
C	VAL57
C	GLY75
C	THR77
C	ALA102
C	PRO103
C	ASN104
C	PHE105
C	PHE217
C	HOH529

site_id	BC1
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NAI D 504

Chain	Residue
D	VAL57
D	GLY75
D	THR77
D	ALA102
D	PRO103
D	ASN104
D	PHE105
D	PHE217
D	HOH510
D	HOH511
D	HOH524
D	HOH527
D	HOH546
D	HOH580
C	SER166
C	THR167
C	HOH505
D	GLY7
D	LYS9
D	GLY10
D	LYS11
D	VAL12
D	ASP33
D	ALA34
D	PHE52
D	THR53

site_id	BC2
Number of Residues	19
Details	BINDING SITE FOR RESIDUE NAI E 505

Chain	Residue
E	GLY7
E	LYS9
E	GLY10
E	LYS11
E	VAL12
E	ASP33
E	ALA34
E	PHE52
E	THR53
E	VAL57
E	GLY75
E	THR76
E	THR77
E	ALA102
E	PRO103
E	ASN104
E	PHE105
E	PHE217
E	HOH507

site_id	BC3
Number of Residues	18
Details	BINDING SITE FOR RESIDUE NAI F 506

Chain	Residue
F	LEU6
F	GLY7
F	GLY10
F	LYS11
F	VAL12
F	ASP33
F	ALA34
F	PHE52
F	THR53
F	VAL57
F	GLY75
F	THR76
F	THR77
F	ALA102
F	PRO103
F	ASN104
F	PHE105
F	HOH513

site_id	BC4
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NAI G 507

Chain	Residue
G	LEU6
G	GLY7
G	LYS9
G	GLY10
G	LYS11
G	VAL12
G	LEU32
G	ASP33
G	ALA34
G	PHE52
G	THR53
G	GLY75
G	THR76
G	THR77
G	ALA102
G	PRO103
G	ASN104
G	PHE105
G	PHE217
G	HOH508
G	HOH524
G	HOH563

site_id	BC5
Number of Residues	18
Details	BINDING SITE FOR RESIDUE NAI H 508

Chain	Residue
H	GLY7
H	LYS9
H	GLY10
H	LYS11
H	VAL12
H	ASP33
H	ALA34
H	PHE52
H	THR53
H	VAL57
H	GLY75
H	THR77
H	ALA102
H	PRO103
H	ASN104
H	PHE105
H	PHE217
H	HOH515

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	GLU127-ALA144

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
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	8
Details	Active site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	56
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12962488","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3V","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12962488","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20057050","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1P9L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YL7","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12962488","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1C3V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1P9L","evidenceCode":"ECO:0007744"}]}

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	LYS136
A	HIS132

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

Chain	Residue	Details
B	LYS136
B	HIS132

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

Chain	Residue	Details
C	LYS136
C	HIS132

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

Chain	Residue	Details
D	LYS136
D	HIS132

site_id	CSA5
Number of Residues	2
Details	Annotated By Reference To The Literature 1arz

Chain	Residue	Details
E	LYS136
E	HIS132

site_id	CSA6
Number of Residues	2
Details	Annotated By Reference To The Literature 1arz

Chain	Residue	Details
F	LYS136
F	HIS132

site_id	CSA7
Number of Residues	2
Details	Annotated By Reference To The Literature 1arz

Chain	Residue	Details
G	LYS136
G	HIS132

site_id	CSA8
Number of Residues	2
Details	Annotated By Reference To The Literature 1arz

Chain	Residue	Details
H	LYS136
H	HIS132

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