Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1GZ4

molecular mechanism of 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	5
Details	BINDING SITE FOR RESIDUE MN A 604

Chain	Residue
A	GLU255
A	ASP256
A	ASP279
A	TTN603
A	HOH2148

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

Chain	Residue
B	TTN603
B	HOH2138
B	ARG165
B	GLU255
B	ASP256
B	ASP279

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN C 604

Chain	Residue
C	ARG165
C	GLU255
C	ASP256
C	ASP279
C	TTN603

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

Chain	Residue
D	ARG165
D	GLU255
D	ASP256
D	ASP279
D	TTN603
D	HOH2147

site_id	AC5
Number of Residues	18
Details	BINDING SITE FOR RESIDUE ATP A 601

Chain	Residue
A	ARG165
A	ASN259
A	LEU310
A	GLY311
A	ALA312
A	GLY313
A	GLU314
A	ALA315
A	ASP345
A	LYS346
A	VAL392
A	ALA393
A	GLY394
A	ALA395
A	SER420
A	HOH2078
A	HOH2143
A	HOH2144

site_id	AC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ATP A 602

Chain	Residue
A	HIS154
A	LYS156
A	GLY192
A	ILE193
A	ARG194
A	ARG197
A	ILE479
A	LEU480
A	ASN482
A	ARG542
A	TYR552
A	ARG556
A	HOH2145

site_id	AC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE TTN A 603

Chain	Residue
A	TYR112
A	ARG165
A	LEU167
A	LYS183
A	GLU255
A	ASP256
A	ASP279
A	ASN421
A	ASN466
A	ASN467
A	MN604
A	HOH2146
A	HOH2147

site_id	AC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE FUM A 605

Chain	Residue
A	GLN64
A	ARG67
A	ARG91
A	LEU95
A	HOH2023
A	HOH2025
A	HOH2149
A	HOH2150
B	PHE127
B	ARG128
B	HOH2030

site_id	AC9
Number of Residues	20
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	GLY394
B	SER420
B	HOH2130
B	HOH2131
B	HOH2132
B	HOH2133
B	HOH2134
B	HOH2135
B	HOH2136

site_id	BC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE ATP B 602

Chain	Residue
B	GLY192
B	ILE193
B	ARG194
B	ARG197
B	ILE479
B	LEU480
B	ARG542
B	ARG556
B	HOH2137
B	HIS154
B	LYS156

site_id	BC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE TTN B 603

Chain	Residue
B	TYR112
B	ARG165
B	LEU167
B	LYS183
B	GLU255
B	ASP256
B	ASP279
B	ASN421
B	ASN466
B	ASN467
B	MN604
B	HOH2113
B	HOH2136

site_id	BC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE FUM B 605

Chain	Residue
A	PHE127
A	ARG128
B	GLN64
B	ARG67
B	ARG91
B	LEU95
B	HOH2019
B	HOH2139
B	HOH2140
B	HOH2141
B	HOH2142

site_id	BC4
Number of Residues	18
Details	BINDING SITE FOR RESIDUE ATP C 601

Chain	Residue
C	ARG165
C	LEU167
C	ASN259
C	ALA312
C	GLY313
C	GLU314
C	ALA315
C	ASP345
C	LYS346
C	VAL392
C	ALA393
C	GLY394
C	ALA395
C	SER420
C	HOH2095
C	HOH2125
C	HOH2126
C	HOH2127

site_id	BC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE ATP C 602

Chain	Residue
C	HIS154
C	LYS156
C	GLY192
C	ILE193
C	ARG194
C	ARG197
C	ILE479
C	LEU480
C	ARG542
C	TYR552
C	ARG556
C	HOH2128

site_id	BC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE TTN C 603

Chain	Residue
C	TYR112
C	ARG165
C	LEU167
C	LYS183
C	GLU255
C	ASP256
C	ASP279
C	ASN421
C	ASN466
C	ASN467
C	MN604

site_id	BC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FUM C 605

Chain	Residue
C	GLN64
C	ARG67
C	ARG91
C	LEU95
C	HOH2015
C	HOH2027
C	HOH2129
C	HOH2130
D	PHE127
D	ARG128

site_id	BC8
Number of Residues	18
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	LEU398
D	SER420
D	HOH2093
D	HOH2139
D	HOH2140
D	HOH2141

site_id	BC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ATP D 602

Chain	Residue
A	ASP244
D	HIS154
D	LYS156
D	GLY192
D	ILE193
D	ARG194
D	ARG197
D	ILE479
D	LEU480
D	ASN482
D	ARG542
D	ARG556
D	HOH2142
D	HOH2143
D	HOH2144

site_id	CC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE TTN D 603

Chain	Residue
D	TYR112
D	ARG165
D	LEU167
D	LYS183
D	GLU255
D	ASP256
D	ASP279
D	ASN421
D	ASN466
D	ASN467
D	MN604
D	HOH2145
D	HOH2146

site_id	CC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE FUM D 605

Chain	Residue
C	PHE127
C	ARG128
D	GLN64
D	ARG67
D	ARG91
D	LEU95
D	HOH2018
D	HOH2022
D	HOH2148
D	HOH2149
D	HOH2150

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	SER136	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	ALA189	electrostatic stabiliser, hydrogen bond donor
A	ALA211	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
A	LEU291	metal ligand
A	LEU292	metal ligand
A	GLU314	hydrogen bond acceptor, proton acceptor, proton donor
A	ALA315	metal ligand
A	GLY473	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA2
Number of Residues	8
Details	M-CSA 21

Chain	Residue	Details
B	SER136	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	ALA189	electrostatic stabiliser, hydrogen bond donor
B	ALA211	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
B	LEU291	metal ligand
B	LEU292	metal ligand
B	GLU314	hydrogen bond acceptor, proton acceptor, proton donor
B	ALA315	metal ligand
B	GLY473	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA3
Number of Residues	8
Details	M-CSA 21

Chain	Residue	Details
C	SER136	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	ALA189	electrostatic stabiliser, hydrogen bond donor
C	ALA211	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
C	LEU291	metal ligand
C	LEU292	metal ligand
C	GLU314	hydrogen bond acceptor, proton acceptor, proton donor
C	ALA315	metal ligand
C	GLY473	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA4
Number of Residues	8
Details	M-CSA 21

Chain	Residue	Details
D	SER136	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	ALA189	electrostatic stabiliser, hydrogen bond donor
D	ALA211	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
D	LEU291	metal ligand
D	LEU292	metal ligand
D	GLU314	hydrogen bond acceptor, proton acceptor, proton donor
D	ALA315	metal ligand
D	GLY473	electrostatic stabiliser, hydrogen bond donor

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