Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1GZ3

Molecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004470	molecular_function	malic enzyme activity
A	0004471	molecular_function	malate dehydrogenase (decarboxylating) (NAD+) activity
A	0004473	molecular_function	malate dehydrogenase (decarboxylating) (NADP+) activity
A	0005739	cellular_component	mitochondrion
A	0005759	cellular_component	mitochondrial matrix
A	0006108	biological_process	malate metabolic process
A	0008948	molecular_function	oxaloacetate decarboxylase activity
A	0009055	molecular_function	electron transfer activity
A	0016491	molecular_function	oxidoreductase activity
A	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A	0046872	molecular_function	metal ion binding
A	0051287	molecular_function	NAD binding
A	1902031	biological_process	regulation of NADP metabolic process
B	0003824	molecular_function	catalytic activity
B	0004470	molecular_function	malic enzyme activity
B	0004471	molecular_function	malate dehydrogenase (decarboxylating) (NAD+) activity
B	0004473	molecular_function	malate dehydrogenase (decarboxylating) (NADP+) activity
B	0005739	cellular_component	mitochondrion
B	0005759	cellular_component	mitochondrial matrix
B	0006108	biological_process	malate metabolic process
B	0008948	molecular_function	oxaloacetate decarboxylase activity
B	0009055	molecular_function	electron transfer activity
B	0016491	molecular_function	oxidoreductase activity
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0046872	molecular_function	metal ion binding
B	0051287	molecular_function	NAD binding
B	1902031	biological_process	regulation of NADP metabolic process
C	0003824	molecular_function	catalytic activity
C	0004470	molecular_function	malic enzyme activity
C	0004471	molecular_function	malate dehydrogenase (decarboxylating) (NAD+) activity
C	0004473	molecular_function	malate dehydrogenase (decarboxylating) (NADP+) activity
C	0005739	cellular_component	mitochondrion
C	0005759	cellular_component	mitochondrial matrix
C	0006108	biological_process	malate metabolic process
C	0008948	molecular_function	oxaloacetate decarboxylase activity
C	0009055	molecular_function	electron transfer activity
C	0016491	molecular_function	oxidoreductase activity
C	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C	0046872	molecular_function	metal ion binding
C	0051287	molecular_function	NAD binding
C	1902031	biological_process	regulation of NADP metabolic process
D	0003824	molecular_function	catalytic activity
D	0004470	molecular_function	malic enzyme activity
D	0004471	molecular_function	malate dehydrogenase (decarboxylating) (NAD+) activity
D	0004473	molecular_function	malate dehydrogenase (decarboxylating) (NADP+) activity
D	0005739	cellular_component	mitochondrion
D	0005759	cellular_component	mitochondrial matrix
D	0006108	biological_process	malate metabolic process
D	0008948	molecular_function	oxaloacetate decarboxylase activity
D	0009055	molecular_function	electron transfer activity
D	0016491	molecular_function	oxidoreductase activity
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D	0046872	molecular_function	metal ion binding
D	0051287	molecular_function	NAD binding
D	1902031	biological_process	regulation of NADP metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE OXL A 603

Chain	Residue
A	ARG165
A	MN604
A	HOH2129
A	HOH2208
A	HOH2264
A	LEU167
A	LYS183
A	GLU255
A	ASP256
A	ASP279
A	ASN421
A	ASN466
A	ASN467

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN A 604

Chain	Residue
A	ARG165
A	GLU255
A	ASP256
A	ASP279
A	OXL603
A	HOH2265

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE OXL B 603

Chain	Residue
B	ARG165
B	LYS183
B	GLU255
B	ASP256
B	ASP279
B	ASN421
B	ASN466
B	ASN467
B	MN604
B	HOH2234
B	HOH2286

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN B 604

Chain	Residue
B	ARG165
B	GLU255
B	ASP256
B	ASP279
B	OXL603
B	HOH2287

site_id	AC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE OXL C 603

Chain	Residue
C	ARG165
C	LEU167
C	LYS183
C	GLU255
C	ASP256
C	ASP279
C	ASN421
C	ASN466
C	ASN467
C	MN604
C	HOH2249
C	HOH2293
C	HOH2298

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN C 604

Chain	Residue
C	ARG165
C	GLU255
C	ASP256
C	ASP279
C	OXL603
C	HOH2299

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE OXL D 603

Chain	Residue
D	ARG165
D	LEU167
D	LYS183
D	GLU255
D	ASP256
D	ASP279
D	ASN421
D	ASN466
D	ASN467
D	MN604
D	HOH2293
D	HOH2298

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN D 604

Chain	Residue
D	ARG165
D	GLU255
D	ASP256
D	ASP279
D	OXL603
D	HOH2299

site_id	AC9
Number of Residues	24
Details	BINDING SITE FOR RESIDUE ATP A 601

Chain	Residue
A	ARG165
A	LEU167
A	ASN259
A	ALA312
A	GLY313
A	GLU314
A	ALA315
A	ASP345
A	LYS346
A	VAL392
A	ALA393
A	GLY394
A	ALA395
A	LEU398
A	SER420
A	HOH2116
A	HOH2186
A	HOH2256
A	HOH2258
A	HOH2259
A	HOH2260
A	HOH2261
A	HOH2262
A	HOH2263

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FUM A 605

Chain	Residue
A	ARG91
A	HOH2028
A	HOH2032
A	HOH2266
A	HOH2267
B	PHE127
A	GLN64
A	ARG67

site_id	BC2
Number of Residues	24
Details	BINDING SITE FOR RESIDUE ATP B 601

Chain	Residue
B	ARG165
B	ASN259
B	GLY311
B	ALA312
B	GLY313
B	GLU314
B	ALA315
B	ASP345
B	LYS346
B	VAL392
B	ALA393
B	ALA395
B	LEU398
B	HOH2274
B	HOH2275
B	HOH2276
B	HOH2277
B	HOH2278
B	HOH2280
B	HOH2281
B	HOH2282
B	HOH2283
B	HOH2284
B	HOH2285

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FUM B 605

Chain	Residue
A	PHE127
A	ARG128
B	GLN64
B	ARG67
B	ARG91
B	HOH2288
B	HOH2289
B	HOH2290

site_id	BC4
Number of Residues	25
Details	BINDING SITE FOR RESIDUE ATP C 601

Chain	Residue
C	ARG165
C	ASN259
C	GLY311
C	ALA312
C	GLY313
C	GLU314
C	ALA315
C	ASP345
C	LYS346
C	VAL392
C	ALA393
C	GLY394
C	ALA395
C	SER420
C	HOH2136
C	HOH2152
C	HOH2289
C	HOH2290
C	HOH2291
C	HOH2292
C	HOH2293
C	HOH2294
C	HOH2295
C	HOH2296
C	HOH2297

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FUM C 605

Chain	Residue
C	GLN64
C	ARG67
C	ARG91
C	HOH2037
C	HOH2043
C	HOH2300
D	PHE127
D	ARG128

site_id	BC6
Number of Residues	24
Details	BINDING SITE FOR RESIDUE ATP D 601

Chain	Residue
D	ARG165
D	ASN259
D	GLY311
D	ALA312
D	GLY313
D	GLU314
D	ALA315
D	ASP345
D	LYS346
D	VAL392
D	ALA393
D	GLY394
D	ALA395
D	LEU398
D	HOH2287
D	HOH2288
D	HOH2289
D	HOH2291
D	HOH2292
D	HOH2293
D	HOH2294
D	HOH2295
D	HOH2296
D	HOH2297

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FUM D 605

Chain	Residue
C	PHE127
D	GLN64
D	ARG67
D	ILE88
D	ARG91
D	HOH2031
D	HOH2036
D	HOH2300

Functional Information from PROSITE/UniProt

site_id	PS00331
Number of Residues	17
Details	MALIC_ENZYMES Malic enzymes signature. FnDDiqGTAaVaLAGLL

Chain	Residue	Details
A	PHE276-LEU292

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12121650","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GZ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GZ4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10700286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QR6","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10700286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12121650","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GZ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GZ4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10700286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QR6","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QR6","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QR6","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PJ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	20
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	3
Details	Annotated By Reference To The Literature 1do8

Chain	Residue	Details
A	ASP278
A	LYS183
A	TYR112

site_id	CSA2
Number of Residues	3
Details	Annotated By Reference To The Literature 1do8

Chain	Residue	Details
B	ASP278
B	LYS183
B	TYR112

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1do8

Chain	Residue	Details
C	ASP278
C	LYS183
C	TYR112

site_id	CSA4
Number of Residues	3
Details	Annotated By Reference To The Literature 1do8

Chain	Residue	Details
D	ASP278
D	LYS183
D	TYR112

site_id	MCSA1
Number of Residues	8
Details	M-CSA 21

Chain	Residue	Details
A	TYR112	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	ARG165	electrostatic stabiliser, hydrogen bond donor
A	LYS183	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
A	GLU255	metal ligand
A	ASP256	metal ligand
A	ASP278	hydrogen bond acceptor, proton acceptor, proton donor
A	ASP279	metal ligand
A	ASN421	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA2
Number of Residues	8
Details	M-CSA 21

Chain	Residue	Details
B	TYR112	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	ARG165	electrostatic stabiliser, hydrogen bond donor
B	LYS183	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
B	GLU255	metal ligand
B	ASP256	metal ligand
B	ASP278	hydrogen bond acceptor, proton acceptor, proton donor
B	ASP279	metal ligand
B	ASN421	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA3
Number of Residues	8
Details	M-CSA 21

Chain	Residue	Details
C	TYR112	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	ARG165	electrostatic stabiliser, hydrogen bond donor
C	LYS183	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
C	GLU255	metal ligand
C	ASP256	metal ligand
C	ASP278	hydrogen bond acceptor, proton acceptor, proton donor
C	ASP279	metal ligand
C	ASN421	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA4
Number of Residues	8
Details	M-CSA 21

Chain	Residue	Details
D	TYR112	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	ARG165	electrostatic stabiliser, hydrogen bond donor
D	LYS183	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
D	GLU255	metal ligand
D	ASP256	metal ligand
D	ASP278	hydrogen bond acceptor, proton acceptor, proton donor
D	ASP279	metal ligand
D	ASN421	electrostatic stabiliser, hydrogen bond donor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)