Structure of PDB 6oxd Chain A

Receptor sequence

>6oxdA (length=736) Species: 1773 (Mycobacterium tuberculosis)

PVIGSFAGVPLHSERAAQSPTEAAVHTHVAAAAAAHGYTPEQLVWHTPEG
IDVTPVYIAADRAAAEAEGYPLHSFPGEPPFVRGPYPTMYVNQPWTIRQY
AGFSTAADSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVQGDVGMA
GVAIDSILDMRQLFDGIDLSTVSVSMTMNGAVLPILALYVVAAEEQGVAP
EQLAGTIQNDILKEFMVRNTYIYPPKPSMRIISDIFAYTSAKMPKFNSIS
ISGYHIQEAGATADLELAYTLADGVDYIRAGLNAGLDIDSFAPRLSFFWG
IGMNFFMEVAKLRAGRLLWSELVAQFAPKSAKSLSLRTHSQTSGWSLTAQ
DVFNNVARTCIEAMAATQGHTQSLHTNALDEALALPTDFSARIARNTQLV
LQQESGTTRPIDPWGGSYYVEWLTHRLARRARAHIAEVAEHGGMAQAISD
GIPKLRIEEAAARTQARIDSGQQPVVGVNKYQVPEDHEIEVLKVENSRVR
AEQLAKLQRLRAGRDEPAVRAALAELTRAAAELGNNLLALAIDAARAQAT
VGEISEALEKVYGRHRAEIRTISGVYRDEVGKAPNIAAATELVEKFAEAD
GRRPRILIAKMGQDGHDRGQKVIATAFADIGFDVDVGSLFSTPEEVARQA
ADNDVHVIGVSSLAAGHLTLVPALRDALAQVGRPDIMIVVGGVIPPGDFD
ELYAAGATAIFPPGTVIADAAIDLLHRLAERLGYTL

3D structure

• PDB: 6oxd Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair.
• Chain: A
• Resolution: 2.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y105 Y259 H260 K623 D627 H629
• Catalytic site (residue number reindexed from 1): Y100 Y254 H255 K610 D614 H616
• Enzyme Commision number: 5.4.99.2: methylmalonyl-CoA mutase.

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	B12	A	Y105 L135 H138 A155 R223 E263 G349 W350 E386 A387 A389 L390 G628 H629 D630 R631 S674 L676 A678 G704 G705 F724 P725 T728	Y100 L130 H133 A150 R218 E258 G344 W345 E381 A382 A384 L385 G615 H616 D617 R618 S661 L663 A665 G691 G692 F711 P712 T715
BS02	NJS	A	Y91 T93 M94 Q98 T101 R103 Y105 S180 T182 T211 R223 H260 R299 S301 F303 R342 T343 H344 Q346 Q377	Y86 T88 M89 Q93 T96 R98 Y100 S175 T177 T206 R218 H255 R294 S296 F298 R337 T338 H339 Q341 Q372

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004494 methylmalonyl-CoA mutase activity
• GO:0016853 isomerase activity
• GO:0016866 intramolecular transferase activity
• GO:0031419 cobalamin binding
• GO:0046872 metal ion binding

Biological Process

• GO:0019678 propionate metabolic process, methylmalonyl pathway

Cellular Component

• GO:0005737 cytoplasm
• GO:0005886 plasma membrane

External links

• PDB: RCSB:6oxd, PDBe:6oxd, PDBj:6oxd
• PDBsum: 6oxd
• PubMed: 31672889
• UniProt: P9WJK5|MUTB_MYCTU Probable methylmalonyl-CoA mutase large subunit (Gene Name=mutB)