Structure of PDB 1do8 Chain D

Receptor sequence

>1do8D (length=553) Species: 9606 (Homo sapiens)

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

3D structure

• PDB: 1do8 Structure of a closed form of human malic enzyme and implications for catalytic mechanism.
• Chain: D
• Resolution: 2.2 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y3112 R3165 K3183 E3255 D3256 D3278 D3279 N3421
• 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	NAD	D	D3244 R3245 G3247	D224 R225 G227
BS02	OXL	D	R3165 L3167 N3421	R145 L147 N401
BS03	MN	D	E3255 D3256 D3279	E235 D236 D259
BS04	NAD	D	R3165 L3167 G3168 N3259 T3283 G3311 A3312 G3313 E3314 A3315 D3345 K3346 V3392 A3393 L3398 L3419 N3421 N3466 N3467	R145 L147 G148 N239 T263 G291 A292 G293 E294 A295 D325 K326 V372 A373 L378 L399 N401 N446 N447
BS05	NAD	D	H3154 R3194 R3197 L3480 R3542 R3556	H134 R174 R177 L460 R522 R536

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:1do8, PDBe:1do8, PDBj:1do8
• PDBsum: 1do8
• PubMed: 10700286
• UniProt: P23368|MAOM_HUMAN NAD-dependent malic enzyme, mitochondrial (Gene Name=ME2)