Structure of PDB 1dms Chain A

Receptor sequence

>1dmsA (length=766) Species: 1061 (Rhodobacter capsulatus)

LANGTVMSGSHWGVFTATVENGRATAFTPWEKDPHPTPMLEGVLDSIYSP
TRIKYPMVRREFLEKGVNADRSTRGNGDFVRVSWDQALDLVAAEVKRVEE
TYGPQGVFGGSYGWKSPGRLHNCTTLLRRMLTLAGGYVNGAGDYSTGAAQ
VIMPHVVGTLEVYEQQTAWPVLAENTEVMVFWAADPIKTSQIGWVIPEHG
AYPGLEALKAKGTKVIVIDPVRTKTVEFFGADHVTPKPQTDVAIMLGMAH
TLVAEDLYDKDFIANYTSGFDKFLPYLMGETDSTPKTAEWASDISGVPAE
TIKELARLFKSKRTMLAAGWSMQRMHHGEQAHWMLVTLASMLGQIGLPGG
GFGLSYHYSGGGTPSSSGPALSGITDGGASVIPVARVVDMLENPGAEFDF
NGTRSKFPDVKMAYWVGGNPFVHHQDRNRMVKAWEKLETFIVHDFQWTPT
ARHADIVLPATTSYERNDIETIGDYSNTGILAMKKIVEPLYEARSDYDIF
AAVAERLGKGKEFTEGKDEMGWIKSFYDDAAKQGKAGGVEMPAFDAFWAE
GIVEFPVTDGADFVRYASFREDPLLNPLGTPTGLIEIYSKNIEKMGYDDC
PAHPTWMEPLERLDGPGAKYPLHIAASHPFNRLHSQLNGTVLREGYAVQG
HEPCLMHPDDAAARGIADGDVVRVHNDRGQILTGVKVTDAVMKGVIQIYE
GGWYDPSDVTEAGTLDKYGDVNVLSADIGTSKLAQGNCGQTVLAEVEKYT
GPAVTLTGFVAPKAAE

3D structure

• PDB: 1dms Crystal structure of dimethyl sulfoxide reductase from Rhodobacter capsulatus at 1.88 A resolution.
• Chain: A
• Resolution: 1.88 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): M41 Y114 W116 D145 S147 T148 V153 I154 W322 S357 Y358 H359 Y360
• Catalytic site (residue number reindexed from 1): M39 Y112 W114 D143 S145 T146 V151 I152 W320 S355 Y356 H357 Y358
• Enzyme Commision number: 1.7.2.3: trimethylamine-N-oxide reductase.
  1.8.5.3: respiratory dimethylsulfoxide reductase.

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	PGD	A	Y114 G115 W116 K117 S118 C125 Y146 S147 R326 G432 G433 H438 H458 D459 F460 R481 D511 A641 H643 H649 S650 Q651 E715 N737 G754	Y112 G113 W114 K115 S116 C123 Y144 S145 R324 G417 G418 H423 H443 D444 F445 R466 D496 A626 H628 H634 S635 Q636 E700 N722 G739
BS02	PGD	A	W116 S147 A185 K190 T191 I220 D221 P222 P240 D243 W322 S323 R326 M327 H359 S642 H643 P644 L648 H649 Q755	W114 S145 A183 K188 T189 I218 D219 P220 P238 D241 W320 S321 R324 M325 H357 S627 H628 P629 L633 H634 Q740
BS03	2MO	A	Y114 W116 Y146 S147	Y112 W114 Y144 S145

Gene Ontology

Molecular Function

• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0030151 molybdenum ion binding
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0050626 trimethylamine-N-oxide reductase (cytochrome c) activity

Biological Process

• GO:0009061 anaerobic respiration

Cellular Component

• GO:0030288 outer membrane-bounded periplasmic space
• GO:0042597 periplasmic space

External links

• PDB: RCSB:1dms, PDBe:1dms, PDBj:1dms
• PDBsum: 1dms
• PubMed: 8890912
• UniProt: Q52675|DSTOR_RHOCA Dimethyl sulfoxide/trimethylamine N-oxide reductase (Gene Name=dorA)