Structure of PDB 5l46 Chain B

Receptor sequence
>5l46B (length=808) Species: 9606 (Homo sapiens) [Search protein sequence]
KDRAETVIIGGGCVGVSLAYHLAKAGMKDVVLLEKSELTAGSTWHAAGLT
TYFHPGINLKKIHYDSIKLYEKLEEETGQVVGFHQPGSIRLATTPVRVDE
FKYQMTRTGWHATEQYLIEPEKIQEMFPLLNMNKVLAGLYNPGDGHIDPY
SLTMALAAGARKCGALLKYPAPVTSLKARSDGTWDVETPQGSMRANRIVN
AAGFWAREVGKMIGLEHPLIPVQHQYVVTSTIPEVKALKRELPVLRDLEG
SYYLRQERDGLLFGPYESQEKMKVQDSWVTNGVPPGFGKELFESDLDRIM
EHIKAAMEMVPVLKKADIINVVNGPITYSPDILPMVGPHQGVRNYWVAIG
FGYGIIHAGGVGKYLSDWILHGEPPFDLIELDPNRYGKWTTTQYTEAKAR
ESYGFNNIVGYPKEERFAGRPTQRVSGLYQRLESKCSMGFHAGWEQPHWF
YKPGQDTQYRPSFRRTNWFEPVGSEYKQVMQRVAVTDLSPFGKFNIKGQD
SIRLLDHLFANVIPKVGFTNISHMLTPKGRVYAELTVSHQSPGEFLLITG
SGSELHDLRWIEEEAVKGGYDVEIKNITDELGVLGVAGPQARKVLQKLTS
EDLSDDVFKFLQTKSLKVSNIPVTAIRISYTGELGWELYHRREDSVALYD
AIMNAGQEEGIDNFGTYAMNALRLEKAFRAWGLEMNCDTNPLEAGLEYFV
KLNKPADFIGKQALKQIKAKGLKRRLVCLTLATDDVDPEGNESIWYNGKV
VGNTTSGSYSYSIQKSLAFAYVPVQLSEVGQQVEVELLGKNYPAVIIQEP
LVLTEPTR
3D structure
PDB5l46 Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant.
ChainB
Resolution3.09 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) T97 E146 H270 Y299 E580
Catalytic site (residue number reindexed from 1) T51 E100 H224 Y253 E534
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 I55 G56 G57 G58 V60 L79 E80 K81 G87 S88 T89 H91 L95 V219 A248 G249 W251 Y272 I372 F397 Y399 G400 I401 I402 I9 G10 G11 G12 V14 L33 E34 K35 G41 S42 T43 H45 L49 V173 A202 G203 W205 Y226 I326 F351 Y353 G354 I355 I356
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0047865 dimethylglycine dehydrogenase activity
Biological Process
GO:0006579 amino-acid betaine catabolic process
GO:0019695 choline metabolic process
GO:0042426 choline catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5l46, PDBe:5l46, PDBj:5l46
PDBsum5l46
PubMed27486859
UniProtQ9UI17|M2GD_HUMAN Dimethylglycine dehydrogenase, mitochondrial (Gene Name=DMGDH)

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