Structure of PDB 1efk Chain D

Receptor sequence

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

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

3D structure

• PDB: 1efk Structure of a closed form of human malic enzyme and implications for catalytic mechanism.
• Chain: D
• Resolution: 2.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y112 R165 K183 E255 D256 D278 D279 N421
• 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	D244 R245	D224 R225
BS02	MG	D	E255 D256 D279	E235 D236 D259
BS03	NAD	D	R165 L167 G168 N259 T283 G311 A312 G313 E314 A315 D345 K346 V392 A393 A395 L398 L419 N421	R145 L147 G148 N239 T263 G291 A292 G293 E294 A295 D325 K326 V372 A373 A375 L378 L399 N401
BS04	NAD	D	H154 R194 I479 L480 R542 Y552 R556	H134 R174 I459 L460 R522 Y532 R536
BS05	MAK	D	R165 L167 E255 D256 D279 N421 N467	R145 L147 E235 D236 D259 N401 N447

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