Structure of PDB 1ogy Chain A

Receptor sequence

>1ogyA (length=789) Species: 1063 (Cereibacter sphaeroides)

IRWSKAPCRFCGTGCGVMVGTRDGQVVATHGDTQAEVNRGLNCVKGYFLS
KIMYGEDRLTTPLLRMKDGVYHKEGEFAPVSWDEAFDVMAAQAKLVLKEK
APEAVGMFGSGQWTIWEGYAASKLMRAGFRSNNLDPNARHCMASAATAFM
RTFGMDEPMGCYDDFEAADAFVLWGSNMAEMHPILWSRLTDRRLSHEHVR
VAVLSTFTHRSSDLSDTPIIFRPGTDRAILNYIAHHIISTGRVNRDFVDR
HTNFALGATDIGYGLRPEHQLQLAAKGAADAGAMTPTDFETFAALVSEYT
LEKAAEISGVEPALLEELAELYADPDRKWMSLWTMGFNQHVRGVWANHMV
YNLHLLTGKISEPGNSPFSLTGQPFACGTAREVGTFAHRLPADMVVTNPE
HRAHAEEIWKLPAGLLPDWVGAHAVEQDRKLHDGEINFYWVQVNNNMQAA
PNIDQETYPGYRNPENFIVVSDAYPTVTGRAADLVLPAAMWVEKEGAYGN
AERRTHFWHQLVEAPGEARSDLWQLMEFSKRFTTDEVWPEEILSAAPAYR
GKTLFEVLFANGSVDRFPASDVNPDHANHEAALFGFYPQKGLFEEYAAFG
RGHGHDLAPFDTYHEVRGLHWPVVEGEETRWRYREGFDPYVKPGEGLRFY
GKPDGRAVILGVPYEPPAESPDEEFGFWLVTGRVLEHWHSGSMTLRWPEL
YKAFPGAVCFMHPEDARSRGLNRGSEVRVISRRGEIRTRLETRGRNRMPR
GVVFVPWFDASQLINKVTLDANDPISRQTDFKKCAVKIE

3D structure

• PDB: 1ogy Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase
• Chain: A
• Resolution: 3.2 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): N53 C54 K56 G122 W124 C152 M153 M346 T382 G383 Q384
• Catalytic site (residue number reindexed from 1): N42 C43 K45 G111 W113 C141 M142 M335 T371 G372 Q373
• 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	C19 C22 C26 N53 C54 I195	C8 C11 C15 N42 C43 I184
BS02	MGD	A	R20 Q123 N148 C152 Q350 Q384 V454 N455 N456 A460 S482 D483 A499 M501 D532 T692 R694 W699 H700 S701 S703 W768 N776 F792	R9 Q112 N137 C141 Q339 Q373 V443 N444 N445 A449 S471 D472 A488 M490 D521 T681 R683 W688 H689 S690 S692 W757 N765 F781
BS03	MGD	A	K56 G186 N188 M192 S216 T217 H220 F232 G235 D237 T345 M346 G347 F348 G383 Q384 R694 V695 L696 H698 W699 H700 K793 K794	K45 G175 N177 M181 S205 T206 H209 F221 G224 D226 T334 M335 G336 F337 G372 Q373 R683 V684 L685 H687 W688 H689 K782 K783
BS04	HEC	A	L52 N53 Y58	L41 N42 Y47

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
• GO:0045333 cellular respiration

Cellular Component

• GO:0042597 periplasmic space
• GO:1990204 oxidoreductase complex

External links

• PDB: RCSB:1ogy, PDBe:1ogy, PDBj:1ogy
• PDBsum: 1ogy
• PubMed: 14528294
• UniProt: Q53176|NAPA_CERS4 Periplasmic nitrate reductase (Gene Name=napA)