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1QR6
Asym. Unit
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Asym.Unit (205 KB)
Biol.Unit 1 (386 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL NAD(P)-DEPENDENT MALIC ENZYME
Authors
:
Y. Xu, G. Bhargava, H. Wu, G. Loeber, L. Tong
Date
:
18 Jun 99 (Deposition) - 05 Jul 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Four Domains, Rossmann Fold, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Xu, G. Bhargava, H. Wu, G. Loeber, L. Tong
Crystal Structure Of Human Mitochondrial Nad(P)(+)-Dependen Malic Enzyme: A New Class Of Oxidative Decarboxylases.
Structure V. 7 877 1999
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close entry info
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Hetero Components
(2, 32)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
28
Mod. Amino Acid
SELENOMETHIONINE
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:165 , ASN A:259 , THR A:283 , LEU A:310 , GLY A:311 , ALA A:312 , GLY A:313 , GLU A:314 , ALA A:315 , PHE A:344 , ASP A:345 , LYS A:346 , VAL A:392 , ALA A:393 , GLY A:394 , LEU A:398 , LEU A:419 , SER A:420 , ASN A:421 , GLY A:446 , GLY A:465 , ASN A:467 , HOH A:2008 , HOH A:2048 , HOH A:2275 , HOH A:2398
BINDING SITE FOR RESIDUE NAD A 601
2
AC2
SOFTWARE
HIS A:154 , LYS A:156 , GLY A:192 , ILE A:193 , ARG A:194 , ARG A:197 , ILE A:479 , LEU A:480 , ASN A:482 , ARG A:542 , ARG A:556 , HOH A:2233 , HOH A:2301 , HOH A:2302 , HOH A:2324 , HOH A:2510 , HOH A:2542 , HOH A:2631 , THR B:1243 , ASP B:1244 , ARG B:1248 , ARG B:1484
BINDING SITE FOR RESIDUE NAD A 602
3
AC3
SOFTWARE
ARG B:1165 , ASN B:1259 , THR B:1283 , GLY B:1311 , ALA B:1312 , GLY B:1313 , GLU B:1314 , ALA B:1315 , ASP B:1345 , LYS B:1346 , VAL B:1392 , ALA B:1393 , GLY B:1394 , ALA B:1395 , LEU B:1419 , SER B:1420 , ASN B:1421 , GLY B:1446 , GLY B:1465 , ASN B:1467 , HOH B:2035 , HOH B:2046 , HOH B:2093 , HOH B:2173 , HOH B:2326 , HOH B:2673
BINDING SITE FOR RESIDUE NAD B 1601
4
AC4
SOFTWARE
THR A:243 , ASP A:244 , GLY A:247 , ARG A:248 , ARG A:484 , HIS B:1154 , LYS B:1156 , GLY B:1192 , ILE B:1193 , ARG B:1194 , ARG B:1197 , ILE B:1479 , LEU B:1480 , ASN B:1482 , ARG B:1542 , ARG B:1556 , HOH B:2017 , HOH B:2129 , HOH B:2352 , HOH B:2676 , HOH B:2721
BINDING SITE FOR RESIDUE NAD B 1602
[
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_034104 (P1114L, chain A/B, )
2: VAR_050017 (G1450E, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_034104
P
114
L
MAOM_HUMAN
Polymorphism
16952692
A
B
P
114
1114
L
2
UniProt
VAR_050017
G
450
E
MAOM_HUMAN
Polymorphism
649224
A
B
G
450
1450
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: MALIC_ENZYMES (A:276-292,B:1276-1292)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MALIC_ENZYMES
PS00331
Malic enzymes signature.
MAOM_HUMAN
276-292
2
A:276-292
B:1276-1292
[
close PROSITE info
]
Exons
(15, 30)
Info
All Exons
Exon 1.2 (A:23-36 | B:1023-1036)
Exon 1.3 (A:37-81 | B:1037-1081)
Exon 1.4 (A:81-131 | B:1081-1131)
Exon 1.5 (A:131-156 | B:1131-1156)
Exon 1.6 (A:157-210 | B:1157-1210)
Exon 1.7 (A:211-245 | B:1211-1245)
Exon 1.8 (A:245-282 | B:1245-1282)
Exon 1.9 (A:282-314 | B:1282-1314)
Exon 1.10 (A:315-352 | B:1315-1352)
Exon 1.11 (A:353-391 | B:1353-1391)
Exon 1.12 (A:391-438 | B:1391-1438)
Exon 1.13 (A:439-473 | B:1439-1473)
Exon 1.14 (A:473-496 | B:1473-1496)
Exon 1.15 (A:497-529 | B:1497-1529)
Exon 1.16b (A:530-573 | B:1530-1573)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.16b
16: Boundary 1.16b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000321341
1a
ENSE00001948888
chr18:
48405419-48405678
260
MAOM_HUMAN
-
0
0
-
-
1.2
ENST00000321341
2
ENSE00001222938
chr18:
48422179-48422298
120
MAOM_HUMAN
1-36
36
2
A:23-36
B:1023-1036
14
14
1.3
ENST00000321341
3
ENSE00000996845
chr18:
48434433-48434566
134
MAOM_HUMAN
37-81
45
2
A:37-81
B:1037-1081
45
45
1.4
ENST00000321341
4
ENSE00000996846
chr18:
48439171-48439320
150
MAOM_HUMAN
81-131
51
2
A:81-131
B:1081-1131
51
51
1.5
ENST00000321341
5
ENSE00001151659
chr18:
48442538-48442613
76
MAOM_HUMAN
131-156
26
2
A:131-156
B:1131-1156
26
26
1.6
ENST00000321341
6
ENSE00001151654
chr18:
48443717-48443878
162
MAOM_HUMAN
157-210
54
2
A:157-210
B:1157-1210
54
54
1.7
ENST00000321341
7
ENSE00001151650
chr18:
48444480-48444583
104
MAOM_HUMAN
211-245
35
2
A:211-245
B:1211-1245
35
35
1.8
ENST00000321341
8
ENSE00001151645
chr18:
48446826-48446935
110
MAOM_HUMAN
245-282
38
2
A:245-282
B:1245-1282
38
38
1.9
ENST00000321341
9
ENSE00001151639
chr18:
48447031-48447128
98
MAOM_HUMAN
282-314
33
2
A:282-314
B:1282-1314
33
33
1.10
ENST00000321341
10
ENSE00001151634
chr18:
48447444-48447557
114
MAOM_HUMAN
315-352
38
2
A:315-352
B:1315-1352
38
38
1.11
ENST00000321341
11
ENSE00000950181
chr18:
48450468-48450582
115
MAOM_HUMAN
353-391
39
2
A:353-391
B:1353-1391
39
39
1.12
ENST00000321341
12
ENSE00000950182
chr18:
48452126-48452268
143
MAOM_HUMAN
391-438
48
2
A:391-438
B:1391-1438
48
48
1.13
ENST00000321341
13
ENSE00000950183
chr18:
48458628-48458730
103
MAOM_HUMAN
439-473
35
2
A:439-473
B:1439-1473
35
35
1.14
ENST00000321341
14
ENSE00000950184
chr18:
48465940-48466010
71
MAOM_HUMAN
473-496
24
2
A:473-496
B:1473-1496
24
24
1.15
ENST00000321341
15
ENSE00000950185
chr18:
48466658-48466756
99
MAOM_HUMAN
497-529
33
2
A:497-529
B:1497-1529
33
33
1.16b
ENST00000321341
16b
ENSE00001605064
chr18:
48473387-48474691
1305
MAOM_HUMAN
530-584
55
2
A:530-573
B:1530-1573
44
44
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1qr6a2 (A:23-279)
1b: SCOP_d1qr6b2 (B:1023-1279)
2a: SCOP_d1qr6a1 (A:280-573)
2b: SCOP_d1qr6b1 (B:1280-1573)
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Malic enzyme N-domain
(14)
Protein domain
:
Mitochondrial NAD(P)-dependent malic enzyme
(13)
Human (Homo sapiens) [TaxId: 9606]
(10)
1a
d1qr6a2
A:23-279
1b
d1qr6b2
B:1023-1279
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Mitochondrial NAD(P)-dependent malic enzyme
(13)
Human (Homo sapiens) [TaxId: 9606]
(10)
2a
d1qr6a1
A:280-573
2b
d1qr6b1
B:1280-1573
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1qr6A01 (A:23-277)
1b: CATH_1qr6B01 (B:1023-1277)
2a: CATH_1qr6A02 (A:278-573)
2b: CATH_1qr6B02 (B:1278-1573)
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(
)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain. Chain A
(17)
Human (Homo sapiens)
(11)
1a
1qr6A01
A:23-277
1b
1qr6B01
B:1023-1277
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
1qr6A02
A:278-573
2b
1qr6B02
B:1278-1573
[
close CATH info
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Malic_M_1qr6B01 (B:1280-1535)
1b: PFAM_Malic_M_1qr6B02 (B:1280-1535)
2a: PFAM_malic_1qr6B03 (B:1089-1270)
2b: PFAM_malic_1qr6B04 (B:1089-1270)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Malic_M
(9)
Homo sapiens (Human)
(5)
1a
Malic_M-1qr6B01
B:1280-1535
1b
Malic_M-1qr6B02
B:1280-1535
Clan
:
no clan defined [family: malic]
(9)
Family
:
malic
(9)
Homo sapiens (Human)
(5)
2a
malic-1qr6B03
B:1089-1270
2b
malic-1qr6B04
B:1089-1270
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