Structure of PDB 2jib Chain B

Receptor sequence

>2jibB (length=559) Species: 847 (Oxalobacter formigenes)

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

3D structure

• PDB: 2jib Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases
• Chain: B
• Resolution: 2.2 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	V32 E56	V26 E50
BS02	TPP	B	Y377 A401 N402 M428 G451 D452 S453 A454 F457 N479 G481 I482 Y483	Y371 A395 N396 M422 G445 D446 S447 A448 F451 N473 G475 I476 Y477
BS03	MG	B	D452 N479 G481	D446 N473 G475
BS04	ADP	B	C98 R160 P161 G221 K222 M247 G280 A281 R282 D306 I307 D325 I326	C92 R154 P155 G215 K216 M241 G274 A275 R276 D300 I301 D319 I320
BS05	COA	B	A264 R266 A267 N358 L362 L404 R408 M409 R555 I556	A258 R260 A261 N352 L356 L398 R402 M403 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:2jib, PDBe:2jib, PDBj:2jib
• PDBsum: 2jib
• PubMed: 17637344
• UniProt: P40149|OXC_OXAFO Oxalyl-CoA decarboxylase (Gene Name=oxc)