Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1PJ3

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate pyruvate, cofactor NAD+, Mn++, and allosteric activator 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	PYR603
A	HOH4903

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN B 1604

Chain	Residue
B	PYR1603
B	HOH4902
B	ARG1165
B	GLU1255
B	ASP1256
B	ASP1279

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN C 2604

Chain	Residue
C	ARG2165
C	GLU2255
C	ASP2256
C	ASP2279
C	PYR2603
C	HOH4904

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN D 3604

Chain	Residue
D	ARG3165
D	GLU3255
D	ASP3256
D	ASP3279
D	PYR3603
D	HOH4001

site_id	AC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE PYR 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	NAD601
A	MN604
A	HOH5000

site_id	AC6
Number of Residues	14
Details	BINDING SITE FOR RESIDUE PYR B 1603

Chain	Residue
B	TYR1112
B	ARG1165
B	LEU1167
B	LYS1183
B	GLU1255
B	ASP1256
B	ASP1279
B	ASN1421
B	ASN1466
B	ASN1467
B	NAD1601
B	MN1604
B	HOH4902
B	HOH4964

site_id	AC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE PYR C 2603

Chain	Residue
C	TYR2112
C	ARG2165
C	LEU2167
C	LYS2183
C	GLU2255
C	ASP2256
C	ASP2279
C	ASN2421
C	ASN2466
C	ASN2467
C	NAD2601
C	MN2604
C	HOH4904

site_id	AC8
Number of Residues	14
Details	BINDING SITE FOR RESIDUE PYR D 3603

Chain	Residue
D	TYR3112
D	ARG3165
D	LEU3167
D	LYS3183
D	GLU3255
D	ASP3256
D	ASP3279
D	ASN3421
D	ASN3466
D	ASN3467
D	NAD3601
D	MN3604
D	HOH4001
D	HOH5039

site_id	AC9
Number of Residues	34
Details	BINDING SITE FOR RESIDUE NAD A 601

Chain	Residue
A	GLY446
A	GLY465
A	ASN466
A	ASN467
A	PYR603
A	HOH4045
A	HOH4124
A	HOH4126
A	HOH4186
A	HOH4647
A	HOH4891
A	HOH5144
A	ARG165
A	LEU167
A	GLY168
A	ASN259
A	ASP279
A	THR283
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	LEU398
A	LEU419
A	SER420
A	ASN421

site_id	BC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE NAD A 602

Chain	Residue
A	GLY192
A	ILE193
A	ARG194
A	ARG197
A	ILE479
A	LEU480
A	ASN482
A	ARG542
A	TYR552
A	ARG556
A	HOH4030
D	ASP3244
D	ARG3245
D	GLY3247

site_id	BC2
Number of Residues	31
Details	BINDING SITE FOR RESIDUE NAD B 1601

Chain	Residue
B	ARG1165
B	LEU1167
B	GLY1168
B	ASN1259
B	ASP1279
B	THR1283
B	GLY1311
B	ALA1312
B	GLY1313
B	GLU1314
B	ALA1315
B	ASP1345
B	LYS1346
B	VAL1392
B	ALA1393
B	GLY1394
B	ALA1395
B	LEU1398
B	LEU1419
B	SER1420
B	ASN1421
B	GLY1446
B	GLY1465
B	ASN1466
B	ASN1467
B	PYR1603
B	HOH4075
B	HOH4193
B	HOH4412
B	HOH4611
B	HOH4972

site_id	BC3
Number of Residues	14
Details	BINDING SITE FOR RESIDUE NAD B 1602

Chain	Residue
B	HIS1154
B	LYS1156
B	GLY1192
B	ILE1193
B	ARG1194
B	ARG1197
B	ILE1479
B	LEU1480
B	ARG1542
B	TYR1552
B	ARG1556
C	ASP2244
C	GLY2247
C	HOH4569

site_id	BC4
Number of Residues	31
Details	BINDING SITE FOR RESIDUE NAD C 2601

Chain	Residue
C	ARG2165
C	LEU2167
C	GLY2168
C	ASN2259
C	ASP2279
C	THR2283
C	LEU2310
C	ALA2312
C	GLY2313
C	GLU2314
C	ALA2315
C	ASP2345
C	LYS2346
C	VAL2392
C	ALA2393
C	GLY2394
C	ALA2395
C	LEU2419
C	SER2420
C	ASN2421
C	GLY2446
C	GLY2465
C	ASN2466
C	ASN2467
C	PYR2603
C	HOH4015
C	HOH4125
C	HOH4312
C	HOH4385
C	HOH4469
C	HOH4685

site_id	BC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE NAD C 2602

Chain	Residue
B	ASP1244
B	ARG1245
B	GLY1247
C	HIS2154
C	LYS2156
C	GLY2192
C	ILE2193
C	ARG2194
C	ARG2197
C	ILE2479
C	LEU2480
C	ASN2482
C	ARG2542
C	TYR2552
C	ARG2556
C	HOH4556

site_id	BC6
Number of Residues	30
Details	BINDING SITE FOR RESIDUE NAD D 3601

Chain	Residue
D	ARG3165
D	LEU3167
D	GLY3168
D	ASN3259
D	ASP3279
D	THR3283
D	GLY3311
D	ALA3312
D	GLY3313
D	GLU3314
D	ALA3315
D	ASP3345
D	LYS3346
D	VAL3392
D	ALA3393
D	GLY3394
D	ALA3395
D	LEU3398
D	LEU3419
D	ASN3421
D	GLY3446
D	GLY3465
D	ASN3466
D	ASN3467
D	PYR3603
D	HOH4082
D	HOH4470
D	HOH4477
D	HOH4498
D	HOH5038

site_id	BC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE NAD D 3602

Chain	Residue
A	ASP244
A	ARG245
A	GLY247
D	HIS3154
D	GLY3192
D	ILE3193
D	ARG3194
D	ARG3197
D	ILE3479
D	LEU3480
D	ASN3482
D	ARG3542
D	TYR3552
D	ARG3556

site_id	BC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FUM A 700

Chain	Residue
A	GLN64
A	ARG67
A	ARG91
A	HOH4071
A	HOH4374
A	HOH4394
B	PHE1127
B	ARG1128
B	HOH4198

site_id	BC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE FUM B 1700

Chain	Residue
A	PHE127
B	GLN1064
B	ARG1067
B	ILE1088
B	ARG1091
B	LEU1095
B	HOH4031
B	HOH4038
B	HOH4094
B	HOH4139
B	HOH4332

site_id	CC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FUM C 2700

Chain	Residue
C	GLN2064
C	ARG2067
C	ARG2091
C	LEU2095
C	HOH4005
C	HOH4014
C	HOH4034
C	HOH4036
C	HOH4254
D	PHE3127

site_id	CC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FUM D 3700

Chain	Residue
C	PHE2127
D	GLN3064
D	ARG3067
D	ARG3091
D	HOH4035
D	HOH4059
D	HOH4081
D	HOH4098
D	HOH4119

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	LYS1183
B	ASP1278
B	TYR1112

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

Chain	Residue	Details
C	ASP2278
C	LYS2183
C	TYR2112

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

Chain	Residue	Details
D	ASP3278
D	TYR3112
D	LYS3183

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	SER1136	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	ALA1189	electrostatic stabiliser, hydrogen bond donor
B	ALA1211	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
B	LEU1291	metal ligand
B	LEU1292	metal ligand
B	GLU1314	hydrogen bond acceptor, proton acceptor, proton donor
B	ALA1315	metal ligand
B	GLY1473	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA3
Number of Residues	8
Details	M-CSA 21

Chain	Residue	Details
C	SER2136	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	ALA2189	electrostatic stabiliser, hydrogen bond donor
C	ALA2211	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
C	LEU2291	metal ligand
C	LEU2292	metal ligand
C	GLU2314	hydrogen bond acceptor, proton acceptor, proton donor
C	ALA2315	metal ligand
C	GLY2473	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA4
Number of Residues	8
Details	M-CSA 21

Chain	Residue	Details
D	SER3136	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	ALA3189	electrostatic stabiliser, hydrogen bond donor
D	ALA3211	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
D	LEU3291	metal ligand
D	LEU3292	metal ligand
D	GLU3314	hydrogen bond acceptor, proton acceptor, proton donor
D	ALA3315	metal ligand
D	GLY3473	electrostatic stabiliser, hydrogen bond donor

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