Structure of PDB 4pab Chain B

Receptor sequence

>4pabB (length=824) Species: 10116 (Rattus norvegicus)

EWKDRAETVIIGGGCVGVSLAYHLAKAGMRDVVLLEKSELTAGSTWHAAG
LTTYFHPGINLKKIHYDSIKLYERLEEETGQVVGFHQPGSIRLATTPERV
DEFKYQMTRTNWHATEQYIIEPEKIHELFPLLNMDKILAGLYNPGDGHID
PYSLTMALATGARKYGVLLKYPAPVTSLKPRPDGTWDVETPQGSVRANRI
VNAAGFWAREVGKMIGLDHPLIPVQHQYVVTSTIPEVKALKRELPVLRDL
EGSYYLRQERDGLLFGPYESQEKMKLQASWVAHGVPPGFGKELFESDLDR
ITEHVEAAMEMVPVLKKADIINIVNGPITYSPDILPMVGPHQGVRNYWVA
IGFGYGIIHAGGVGKYLSDWILHGEPPFDLIELDPNRYGKWTTTQYTEAK
ARESYGFNNIVGYPKEERFAGRPTQRVSGLYKILESKCSMGFHAGWEQPH
WFYKPGQDTQYRPSFRRTNWFRPVGSEYKQVMQRVGVIDLSPFGKFNIKG
QDSTQLLDHLCANVIPKVGFTNISHMLTPRGRVYAELTVSHQSPGEFLLI
TGSGSELHDLRWIEEAAVRGGYDVEIRNITDELGVLGVAGPYARRVLQKL
TSEDLSDDVFKFLQTKSLKISDIPVTAIRISYTGELGWELYHRREDSAAL
YERIMNAGQEEGIDNFGTYALNALRLEKAFRAWGSEMNCDTNPLEAGLDY
FIKLNKPADFTGKQALKQIKAKGLKRRLVCLTLATDDVDPEGNESVWYKG
KVIGNTTSGSYSYSIQKSLAFAYVPVELSEVGQQVEVELLGKNYPATIIQ
EPLVLTEPTRTRLQKDGRKSAALE

3D structure

• PDB: 4pab Folate in demethylation: The crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate.
• Chain: B
• Resolution: 1.85 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): T90 E139 H263 Y292 E573
• Catalytic site (residue number reindexed from 1): T53 E102 H226 Y255 E536
• Enzyme Commision number: 1.5.8.4: dimethylglycine dehydrogenase.

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	FAD	B	I48 G49 G51 C52 V53 L72 E73 K74 G80 S81 T82 H84 A85 A86 G87 L88 V212 A241 G242 W244 H263 Y265 G363 I365 F390 Y392 G393 I394 I395	I11 G12 G14 C15 V16 L35 E36 K37 G43 S44 T45 H47 A48 A49 G50 L51 V175 A204 G205 W207 H226 Y228 G326 I328 F353 Y355 G356 I357 I358
BS02	THG	B	I560 E573 T575 I587 F649 L650 Y669 E676 F717 Y737	I523 E536 T538 I550 F612 L613 Y632 E639 F680 Y700

Gene Ontology

Molecular Function

• GO:0005542 folic acid binding
• GO:0016491 oxidoreductase activity
• GO:0047865 dimethylglycine dehydrogenase activity
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0006579 amino-acid betaine catabolic process
• GO:0019695 choline metabolic process
• GO:0035999 tetrahydrofolate interconversion
• GO:0042426 choline catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix

External links

• PDB: RCSB:4pab, PDBe:4pab, PDBj:4pab
• PDBsum: 4pab
• PubMed: 24858690
• UniProt: Q63342|M2GD_RAT Dimethylglycine dehydrogenase, mitochondrial (Gene Name=Dmgdh)