Structure of PDB 1rpn Chain B

Receptor sequence

>1rpnB (length=321) Species: 287 (Pseudomonas aeruginosa)

RSALVTGITGQDGAYLAKLLLEKGYRVHGLVARRSSDTRWRLRELGIEGD
IQYEDGDMADACSVQRAVIKAQPQEVYNLAAQSFVGASWNQPVTTGVVDG
LGVTHLLEAIRQFSPETRFYQASTSEMFGLIQAERQDENTPFYPRSPYGV
AKLYGHWITVNYRESFGLHASSGILFNHESPLRGIEFVTRKVTDAVARIK
LGKQQELRLGNVDAKRDWGFAGDYVEAMWLMLQQDKADDYVVATGVTTTV
RDMCQIAFEHVGLDYRDFLKIDPAFFRPAEVDVLLGNPAKAQRVLGWKPR
TSLDELIRMMVEADLRRVSRE

3D structure

• PDB: 1rpn Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway.
• Chain: B
• Resolution: 2.15 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): T126 S127 E128 Y150 K154
• Catalytic site (residue number reindexed from 1): T124 S125 E126 Y148 K152
• Enzyme Commision number: 4.2.1.47: GDP-mannose 4,6-dehydratase.

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	NDP	B	G9 T11 G12 Q13 D14 R36 D59 M60 L81 A82 A83 S85 A124 S125 T126 Y150 K154 L177 N179 H180 R185	G7 T9 G10 Q11 D12 R34 D57 M58 L79 A80 A81 S83 A122 S123 T124 Y148 K152 L175 N177 H178 R183
BS02	GDP	B	F86 E128 N179 E188 F189 V190 K193 L211 G212 N213 R218 F277 R279 E282	F84 E126 N177 E186 F187 V188 K191 L209 G210 N211 R216 F275 R277 E280
BS03	NDP	B	R35 S37	R33 S35

Gene Ontology

Molecular Function

• GO:0008446 GDP-mannose 4,6-dehydratase activity
• GO:0016829 lyase activity
• GO:0070401 NADP+ binding

Biological Process

• GO:0009103 lipopolysaccharide biosynthetic process
• GO:0009243 O antigen biosynthetic process
• GO:0019306 GDP-D-rhamnose biosynthetic process
• GO:0019673 GDP-mannose metabolic process
• GO:0042351 'de novo' GDP-L-fucose biosynthetic process

External links

• PDB: RCSB:1rpn, PDBe:1rpn, PDBj:1rpn
• PDBsum: 1rpn
• PubMed: 14739333
• UniProt: Q51366|GM4D_PSEAE GDP-mannose 4,6-dehydratase (Gene Name=gmd)