Structure of PDB 2gyi Chain B

Receptor sequence

>2gyiB (length=385) Species: 1963 (Streptomyces olivochromogenes)

YQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVT
FHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDG
GFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVR
VALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAF
IERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGI
KYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWAS
AAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLA
DRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR

3D structure

• PDB: 2gyi Design, Synthesis, and Characterization of a Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex
• Chain: B
• Resolution: 1.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H53 D56 M87 E180 K182 E216 H219 D244 D254 D256 D286
• Catalytic site (residue number reindexed from 1): H52 D55 M86 E179 K181 E215 H218 D243 D253 D255 D285
• Enzyme Commision number: 5.3.1.5: xylose isomerase.

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	MG	B	E180 E216 D244 D286	E179 E215 D243 D285
BS02	MG	B	E216 H219	E215 H218
BS03	HYA	B	H53 F93 W136 E180 D286	H52 F92 W135 E179 D285	MOAD: Ki<100nM PDBbind-CN: -logKd/Ki=7.00,Ki<=100nM

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0009045 xylose isomerase activity
• GO:0016853 isomerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0042732 D-xylose metabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2gyi, PDBe:2gyi, PDBj:2gyi
• PDBsum: 2gyi
• PubMed: 7893671
• UniProt: P15587|XYLA_STROL Xylose isomerase (Gene Name=xylA)