Structure of PDB 6h0p Chain A

Receptor sequence

>6h0pA (length=375) Species: 3702 (Arabidopsis thaliana)

VDLDGKPIQPLTICMIGAGGFIGSHLCEKLLTETPHKVLALDVYNDKIKH
LLEPDTVEWSGRIQFHRINIKHDSRLEGLVKMADLIINLAAIATPADYNT
RPLDTIYSNFIDALPVVKYCSENNKRLIHFSTCEVYGKTIGSFLPKDHPL
RDDPAFYVLKEDISPCIFGSIEKQRWSYACAKQLIERLVYAEGAENGLEF
TIVRPFNWIGPRMDFIPGIDGPSEGVPRVLACFSNNLLRREPLKLVDGGE
SQRTFVYINDAIEAVLLMIENPERANGHIFNVGNPNNEVTVRQLAEMMTE
VYAKVSGEGAIESPTVDVSSKEFYGEGYDDSDKRIPDMTIINRQLGWNPK
TSLWDLLESTLTYQHRTYAEAVKKA

3D structure

• PDB: 6h0p Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis.
• Chain: A
• Resolution: 3.47 Å

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	NAD	A	G24 G27 F28 I29 D49 N76 I77 L96 A97 A98 A100 F137 Y185 K189	G17 G20 F21 I22 D42 N69 I70 L89 A90 A91 A93 F130 Y178 K182
BS02	UGA	A	P102 Y105 T139 E141 R182 Y185 N214 R235 V236 C239 F240 V253 R260 V298 F330 Y331 Y335 D337 R341	P95 Y98 T132 E134 R175 Y178 N207 R228 V229 C232 F233 V246 R253 V291 F323 Y324 Y328 D330 R334

Gene Ontology

Molecular Function

• GO:0016831 carboxy-lyase activity
• GO:0042802 identical protein binding
• GO:0042803 protein homodimerization activity
• GO:0046982 protein heterodimerization activity
• GO:0048040 UDP-glucuronate decarboxylase activity
• GO:0051287 NAD binding
• GO:0102765 UDP-D-apiose synthase activity

Biological Process

• GO:0009226 nucleotide-sugar biosynthetic process
• GO:0010396 rhamnogalacturonan II metabolic process
• GO:0033320 UDP-D-xylose biosynthetic process
• GO:0033352 UDP-D-apiose biosynthetic process
• GO:0071555 cell wall organization

Cellular Component

• GO:0005737 cytoplasm
• GO:0005777 peroxisome
• GO:0005829 cytosol

External links

• PDB: RCSB:6h0p, PDBe:6h0p, PDBj:6h0p
• PDBsum: 6h0p
• PubMed: 31844840
• UniProt: Q9ZUY6|AXS1_ARATH UDP-D-apiose/UDP-D-xylose synthase 1 (Gene Name=AXS1)