Structure of PDB 3ml1 Chain A

Receptor sequence

>3ml1A (length=799) Species: 381666 (Cupriavidus necator H16)

VTDSEVTKLKWSKAPCRFCGTGCGVTVAVKDNKVVATQGDPQAEVNKGLN
CVKGYFLSKIMYGQDRLTRPLMRMKNGKYDKNGDFAPVTWDQAFDEMERQ
FKRVLKEKGPTAVGMFGSGQWTVWEGYAAAKLYKAGFRSNNIDPNARHCM
ASAAAGFMRTFGMDEPMGCYDDFEAADAFVLWGSNMAEMHPILWTRVTDR
RLSHPKTRVVVLSTFTHRCFDLADIGIIFKPQTDLAMLNYIANYIIRNNK
VNKDFVNKHTVFKEGVTDIGYGLRPDHPLQKAAKNASDPGAAKVITFDEF
AKFVSKYDADYVSKLSAVPKAKLDQLAELYADPNIKVMSLWTMGFNQHTR
GTWANNMVYNLHLLTGKIATPGNSPFSLTGQPSACGTAREVGTFSHRLPA
DMVVTNPKHREEAERIWKLPPGTIPDKPGYDAVLQNRMLKDGKLNAYWVQ
VNNNMQAAANLMEEGLPGYRNPANFIVVSDAYPTVTALAADLVLPSAMWV
EKEGAYGNAERRTQFWHQLVDAPGEARSDLWQLVEFAKRFKVEEVWPPEL
IAKKPEYKGKTLYDVLYRNGQVDKFPLKDVNAEYHNAEAKAFGFYLQKGL
FEEYATFGRGHGHDLAPFDAYHEARGLRWPVVNGKETRWRYREGSDPYVK
AGTGFQFYGNPDGKAVIFALPYEPPAESPDKEYPYWLVTGRVLEHWHSGS
MTRRVPELYRSFPNAVVFMHPEDAKALGLRRGVEVEVVSRRGRMRSRIET
RGRDAPPRGLVFVPWFDASQLINKVTLDATCPISLQTDFKKCAVKIVKV

3D structure

• PDB: 3ml1 The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states
• Chain: A
• Resolution: 1.6 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): N50 C51 K53 G119 W121 C149 M150 M343 T379 G380 Q381
• 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 T24 C26 N53 C54	C16 C19 T21 C23 N50 C51
BS02	MGD	A	R20 Q123 N148 H151 C152 Q350 Q384 V454 N455 N456 A460 S482 D483 S499 M501 K505 D532 T692 R694 W699 H700 S701 S703 W768 N776 F792	R17 Q120 N145 H148 C149 Q347 Q381 V451 N452 N453 A457 S479 D480 S496 M498 K502 D529 T689 R691 W696 H697 S698 S700 W765 N773 F789
BS03	MGD	A	K56 W185 G186 N188 M192 S216 T217 F218 H220 F232 D237 T345 M346 G347 F348 G383 Q384 G693 R694 L696 H698 W699 H700 K793	K53 W182 G183 N185 M189 S213 T214 F215 H217 F229 D234 T342 M343 G344 F345 G380 Q381 G690 R691 L693 H695 W696 H697 K790
BS04	HEC	A	L52 Y58	L49 Y55

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:3ml1, PDBe:3ml1, PDBj:3ml1
• PDBsum: 3ml1
• PubMed: 21419779
• UniProt: P39185|NAPA_CUPNH Periplasmic nitrate reductase (Gene Name=napA)