Structure of PDB 1pj3 Chain B

Receptor sequence

>1pj3B (length=553) Species: 9606 (Homo sapiens)

IKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHR
NLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLAC
SQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLG
DLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMG
LYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYR
EKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIA
NLIVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAP
ESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALS
NPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYI
FPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQ
EVSINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVY
EWP

3D structure

• PDB: 1pj3 Crystal structures of substrate complexes of malic enzyme and insights into the catalytic mechanism.
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1112 R1165 K1183 E1255 D1256 D1278 D1279 N1421
• Catalytic site (residue number reindexed from 1): Y92 R145 K163 E235 D236 D258 D259 N401
• Enzyme Commision number: 1.1.1.38: malate dehydrogenase (oxaloacetate-decarboxylating).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MN	B	E1255 D1256 D1279	E235 D236 D259
BS02	PYR	B	R1165 L1167 K1183 D1279 N1421	R145 L147 K163 D259 N401
BS03	NAD	B	R1165 L1167 G1168 N1259 T1283 G1311 A1312 G1313 E1314 A1315 D1345 K1346 A1393 A1395 L1398 L1419 S1420 N1421 G1465 N1466 N1467	R145 L147 G148 N239 T263 G291 A292 G293 E294 A295 D325 K326 A373 A375 L378 L399 S400 N401 G445 N446 N447
BS04	NAD	B	H1154 K1156 I1193 R1194 R1197 I1479 L1480 R1542 R1556	H134 K136 I173 R174 R177 I459 L460 R522 R536
BS05	FUM	B	Q1064 R1067 R1091 L1095	Q44 R47 R71 L75
BS06	NAD	B	D1244 R1245 G1247	D224 R225 G227

Gene Ontology

Molecular Function

• GO:0004470 malic enzyme activity
• GO:0004471 malate dehydrogenase (decarboxylating) (NAD+) activity
• GO:0004473 malate dehydrogenase (decarboxylating) (NADP+) activity
• GO:0008948 oxaloacetate decarboxylase activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0046872 metal ion binding
• GO:0051287 NAD binding

Biological Process

• GO:0006090 pyruvate metabolic process
• GO:0006108 malate metabolic process
• GO:1902031 regulation of NADP metabolic process

Cellular Component

• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:1pj3, PDBe:1pj3, PDBj:1pj3
• PDBsum: 1pj3
• PubMed: 12962632
• UniProt: P23368|MAOM_HUMAN NAD-dependent malic enzyme, mitochondrial (Gene Name=ME2)