Structure of PDB 2v3v Chain A

Receptor sequence

>2v3vA (length=721) Species: 876 (Desulfovibrio desulfuricans)

NRPEKWVKGVCRYCGTGCGVLVGVKDGKAVAIQGDPNNHNAGLLCLKGSL
LIPVLNSKERVTQPLVRRHKGGKLEPVSWDEALDLMASRFRSSIDMYGPN
SVAWYGSGQCLTEESYVANKIFKGGFGTNNVDGNPRLCMASAVGGYVTSF
GKDEPMGTYADIDQATCFFIIGSNTSEAHPVLFRRIARRKQVEPGVKIIV
ADPRRTNTSRIADMHVAFRPGTDLAFMHSMAWVIINEELDNPRFWQRYVN
FMDAEGKPSDFEGYKAFLENYRPEKVAEICRVPVEQIYGAARAFAESAAT
MSLWCMGINQRVQGVFANNLIHNLHLITGQICRPGATSFSLTGQPNACGG
VRDGGALSHLLPAGRAIPNAKHRAEMEKLWGLPEGRIAPEPGYHTVALFE
ALGRGDVKCMIICETNPAHTLPNLNKVHKAMSHPESFIVCIEAFPDAVTL
EYADLVLPPAFWCERDGVYGCGERRYSLTEKAVDPPGQCRPTVNTLVEFA
RRAGVDPQLVNFRNAEDVWNEWRMVSKGTTYDFWGMTRERLRKESGLIWP
CPSEDHPGTSLRYVRGQDPCVPADHPDRFFFYGKPDGRAVIWMRPAKGAA
EEPDAEYPLYLTSMRVIDHWHTATMTGKVPELQKANPIAFVEINEEDAAR
TGIKHGDSVIVETRRDAMELPARVSDVCRPGLIAVPFFDPKKLVNKLFLD
ATDPVSREPEYKICAARVRKA

3D structure

• PDB: 2v3v Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes the Sixth Coordination of the Catalytic Molybdenum.
• Chain: A
• Resolution: 1.99 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K49 S109 C140 M141 A180 M308 T344 G345 Q346
• Catalytic site (residue number reindexed from 1): K47 S107 C138 M139 A178 M306 T342 G343 Q344
• Enzyme Commision number: 1.9.6.1: nitrate reductase (cytochrome).

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	SF4	A	C13 C16 T18 C20 L46 C47 V183	C11 C14 T16 C18 L44 C45 V181
BS02	MGD	A	R14 Q111 C140 Q312 Q346 E416 T417 N418 T422 I443 E444 A445 P461 F463 S615 R617 H623 T624 T626 F689 N697 Y713	R12 Q109 C138 Q310 Q344 E414 T415 N416 T420 I441 E442 A443 P459 F461 S613 R615 H621 T622 T624 F687 N695 Y711
BS03	MGD	A	K49 G174 S175 A180 D204 P205 R206 F220 P222 D225 C307 M308 G309 G345 Q346 M616 R617 I619 H621 W622 H623 K714	K47 G172 S173 A178 D202 P203 R204 F218 P220 D223 C305 M306 G307 G343 Q344 M614 R615 I617 H619 W620 H621 K712

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0008940 nitrate reductase activity
• 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:0050140 nitrate reductase (cytochrome) activity
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006777 Mo-molybdopterin cofactor biosynthetic process
• GO:0042128 nitrate assimilation

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:2v3v, PDBe:2v3v, PDBj:2v3v
• PDBsum: 2v3v
• PubMed: 18327621
• UniProt: P81186|NAPA_DESDA Periplasmic nitrate reductase (Gene Name=napA)