Structure of PDB 2ji8 Chain B

Receptor sequence

>2ji8B (length=556) Species: 847 (Oxalobacter formigenes)

VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHE
QHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSG
SSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTA
VSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARA
ADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPD
NHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQID
IQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVD
GNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDN
TRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFG
FSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYD
MMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVESGRI
KSLNVV

3D structure

• PDB: 2ji8 Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases
• Chain: B
• Resolution: 2.15 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): V31 G33 I34 P35 I36 E56 V79 Y120 E121 E122 A170 M287 G400 G426 M428 D452 N479 G481 I482 K484 G485 A488 P547
• Catalytic site (residue number reindexed from 1): V25 G27 I28 P29 I30 E50 V73 Y114 E115 E116 A164 M281 G394 G420 M422 D446 N473 G475 I476 K478 G479 A482 P541
• Enzyme Commision number: 4.1.1.8: oxalyl-CoA decarboxylase.

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	TPP	B	E56 P82 G83	E50 P76 G77
BS02	TPP	B	Y377 A401 N402 A403 G426 M428 G451 D452 S453 A454 F457 N479 G481 I482 Y483	Y371 A395 N396 A397 G420 M422 G445 D446 S447 A448 F451 N473 G475 I476 Y477
BS03	MG	B	D452 N479 G481	D446 N473 G475
BS04	ADP	B	C98 R160 G221 K222 G223 M247 G280 A281 R282 D306 I307 D325 I326	C92 R154 G215 K216 G217 M241 G274 A275 R276 D300 I301 D319 I320
BS05	FYN	B	A263 A264 T265 R266 A267 L286 N358 L362 G400 L404 R408 M409 S553 R555 I556	A257 A258 T259 R260 A261 L280 N352 L356 G394 L398 R402 M403 S547 R549 I550

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0008949 oxalyl-CoA decarboxylase activity
• GO:0016831 carboxy-lyase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0042802 identical protein binding
• GO:0043531 ADP binding
• GO:0046872 metal ion binding

Biological Process

• GO:0001561 fatty acid alpha-oxidation
• GO:0019752 carboxylic acid metabolic process
• GO:0033611 oxalate catabolic process

External links

• PDB: RCSB:2ji8, PDBe:2ji8, PDBj:2ji8
• PDBsum: 2ji8
• PubMed: 17637344
• UniProt: P40149|OXC_OXAFO Oxalyl-CoA decarboxylase (Gene Name=oxc)