Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1PJ4

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate malate, ATP, 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	15
Details	BINDING SITE FOR RESIDUE MLT A 701

Chain	Residue
A	TYR112
A	ASN466
A	ASN467
A	MN4604
A	HOH4625
A	HOH4631
A	HOH4705
A	THR113
A	ARG165
A	LEU167
A	LYS183
A	GLU255
A	ASP256
A	ASP279
A	ASN421

site_id	AC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE MLT B 1701

Chain	Residue
B	HOH12
B	HOH54
B	HOH504
B	TYR1112
B	ARG1165
B	LEU1167
B	LYS1183
B	GLU1255
B	ASP1256
B	ASP1279
B	ASN1421
B	ASN1466
B	ASN1467
B	MN1604

site_id	AC3
Number of Residues	14
Details	BINDING SITE FOR RESIDUE MLT C 2701

Chain	Residue
C	HOH112
C	HOH538
C	TYR2112
C	THR2113
C	ARG2165
C	LEU2167
C	LYS2183
C	GLU2255
C	ASP2256
C	ASP2279
C	ASN2421
C	ASN2466
C	ASN2467
C	MN2604

site_id	AC4
Number of Residues	14
Details	BINDING SITE FOR RESIDUE MLT D 3701

Chain	Residue
D	HOH10
D	HOH249
D	TYR3112
D	THR3113
D	ARG3165
D	LEU3167
D	LYS3183
D	GLU3255
D	ASP3256
D	ASP3279
D	ASN3421
D	ASN3466
D	ASN3467
D	MN3604

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN A 4604

Chain	Residue
A	ARG165
A	GLU255
A	ASP256
A	ASP279
A	MLT701
A	HOH4625

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN B 1604

Chain	Residue
B	HOH12
B	GLU1255
B	ASP1256
B	ASP1279
B	MLT1701

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN C 2604

Chain	Residue
C	HOH112
C	GLU2255
C	ASP2256
C	ASP2279
C	MLT2701

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN D 3604

Chain	Residue
D	HOH10
D	ARG3165
D	GLU3255
D	ASP3256
D	ASP3279
D	MLT3701

site_id	AC9
Number of Residues	19
Details	BINDING SITE FOR RESIDUE ATP A 4601

Chain	Residue
A	ARG165
A	ASN259
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	HOH4680
A	HOH4690
A	HOH4715
A	HOH4716
A	HOH4760

site_id	BC1
Number of Residues	17
Details	BINDING SITE FOR RESIDUE ATP B 1601

Chain	Residue
B	HOH245
B	HOH272
B	HOH488
B	ARG1165
B	ASN1259
B	GLY1311
B	ALA1312
B	GLY1313
B	GLU1314
B	ALA1315
B	ASP1345
B	LYS1346
B	VAL1392
B	ALA1393
B	GLY1394
B	SER1420
B	HOH23

site_id	BC2
Number of Residues	18
Details	BINDING SITE FOR RESIDUE ATP C 2601

Chain	Residue
C	HOH100
C	HOH120
C	HOH424
C	HOH533
C	HOH538
C	ARG2165
C	ASN2259
C	ALA2312
C	GLY2313
C	GLU2314
C	ALA2315
C	ASP2345
C	LYS2346
C	VAL2392
C	ALA2393
C	GLY2394
C	ALA2395
C	SER2420

site_id	BC3
Number of Residues	20
Details	BINDING SITE FOR RESIDUE ATP D 3601

Chain	Residue
D	HOH28
D	HOH198
D	HOH390
D	HOH460
D	HOH467
D	HOH680
D	ARG3165
D	ASN3259
D	LEU3310
D	GLY3311
D	ALA3312
D	GLY3313
D	GLU3314
D	ALA3315
D	ASP3345
D	LYS3346
D	VAL3392
D	ALA3393
D	GLY3394
D	SER3420

site_id	BC4
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ATP A 4602

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	HOH4647
A	HOH4706
D	HOH513
D	ASP3244

site_id	BC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ATP B 1602

Chain	Residue
B	HOH228
B	HOH252
B	HOH464
B	HIS1154
B	LYS1156
B	GLY1192
B	ARG1194
B	ARG1197
B	ILE1479
B	LEU1480
B	ASN1482
B	ARG1542
B	TYR1552
B	ARG1556
C	ASP2244

site_id	BC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ATP C 2602

Chain	Residue
B	ASP1244
C	HOH561
C	HIS2154
C	LYS2156
C	GLY2192
C	ILE2193
C	ARG2194
C	ARG2197
C	ILE2479
C	LEU2480
C	ARG2542
C	TYR2552
C	ARG2556

site_id	BC7
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ATP D 3602

Chain	Residue
A	ASP244
D	HOH2
D	HOH202
D	HOH348
D	HOH416
D	HIS3154
D	LYS3156
D	GLY3192
D	ILE3193
D	ARG3194
D	ARG3197
D	ILE3479
D	LEU3480
D	ARG3542
D	TYR3552
D	ARG3556

site_id	BC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FUM A 700

Chain	Residue
A	GLN64
A	ARG67
A	ARG91
A	HOH4621
A	HOH4627
A	HOH4694
A	HOH4736
B	ARG1128

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FUM B 1700

Chain	Residue
A	PHE127
A	ARG128
B	HOH39
B	HOH88
B	HOH117
B	HOH138
B	GLN1064
B	ARG1067
B	ARG1091

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

Chain	Residue
C	HOH20
C	HOH31
C	HOH59
C	HOH83
C	GLN2064
C	ARG2067
C	ARG2091
C	LEU2095
D	PHE3127
D	ARG3128

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

Chain	Residue
C	PHE2127
D	HOH53
D	HOH164
D	HOH169
D	HOH280
D	GLN3064
D	ARG3067
D	ARG3091
D	LEU3095

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)