Structure of PDB 1y5i Chain A

Receptor sequence

>1y5iA (length=1244) Species: 562 (Escherichia coli)

SKFLDRFRYFKQKGETFADGHGQLLNTNRDWEDGYRQRWQHDKIVRSTHG
VNCTGSCSWKIYVKNGLVTWETQQTDYPRTRPDLPNHEPRGCPRGASYSW
YLYSANRLKYPMMRKRLMKMWREAKALHSDPVEAWASIIEDADKAKSFKQ
ARGRGGFVRSSWQEVNELIAASNVYTIKNYGPDRVAGFSPIPAMSMVSYA
SGARYLSLIGGTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYII
AWGSNVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQG
TDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYTDMPMLVMLEERDGYYA
AGRMLRAADLVDALGQENNPEWKTVAFNTNGEMVAPNGSIGFRWGEKGKW
NLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENV
LLHKLPVKRLQLADGSTALVTTVYDLTLANYGLERGLNDVNCATSYDDVK
AYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHL
DMNYRGLINMLIFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQR
PARHMNSTSYFYNHSSQWRYETVTAEELLSPMADKSRYTGHLIDFNVRAE
RMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPE
NGKNHPRNLFIWRSNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVK
PEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYEKDDMNTS
DMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTL
PIQHDSAAELAQPLDVKDWKKGECDLIPGKTAPHIMVVERDYPATYERFT
SIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAID
AAEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQ
AQPRKIISSPTWSGLEDEHVSYNAGYTNVHELIPWRTLSGRQQLYQDHQW
MRDFGESLLVYRPPIDTRSVKEVIGQKSNGNQEKALNFLTPHQKWGIHST
YSDNLLMLTLGRGGPVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVV
SQRVPAGMTMMYHAQERIVNLPGSEITQQRGGIHNSVTRITPKPTHMIGG
YAHLAYGFNYYGTVGSNRDEFVVVRKMKNIDWLDGEGNDQVQES

3D structure

• PDB: 1y5i Structural and Biochemical Characterization of a Quinol Binding Site of Escherichia coli Nitrate Reductase A
• Chain: A
• Resolution: 1.9 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R94 P190 W219 Y220 P224 Q580
• Catalytic site (residue number reindexed from 1): R94 P190 W219 Y220 P224 Q580
• Enzyme Commision number: 1.7.5.1: nitrate reductase (quinone).

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	MD1	A	Y220 D222 H546 R713 S714 N715 S719 S720 K722 L771 D772 F773 R774 T788 W791 K794 D822 T1090 H1092 H1098 S1099 T1100 H1163 H1184 N1185 N1217	Y220 D222 H546 R713 S714 N715 S719 S720 K722 L771 D772 F773 R774 T788 W791 K794 D822 T1090 H1092 H1098 S1099 T1100 H1163 H1184 N1185 N1217
BS02	MD1	A	N52 R94 D222 G253 S254 N255 Q258 T259 V280 P282 D283 Q299 D302 G541 A542 G543 L544 W547 V578 G579 P1091 H1092 Q1093 I1097 H1098 R1218	N52 R94 D222 G253 S254 N255 Q258 T259 V280 P282 D283 Q299 D302 G541 A542 G543 L544 W547 V578 G579 P1091 H1092 Q1093 I1097 H1098 R1218
BS03	6MO	A	D222 G579	D222 G579
BS04	SF4	A	H49 V51 C53 G55 C57 W59 G91 C92 G95 P262	H49 V51 C53 G55 C57 W59 G91 C92 G95 P262

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008940 nitrate reductase activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0160182 nitrate reductase (quinone) activity

Biological Process

• GO:0009061 anaerobic respiration
• GO:0019645 anaerobic electron transport chain
• GO:0042126 nitrate metabolic process
• GO:0042128 nitrate assimilation
• GO:0045333 cellular respiration

Cellular Component

• GO:0005886 plasma membrane
• GO:0009325 nitrate reductase complex
• GO:0016020 membrane
• GO:0044799 NarGHI complex
• GO:1990204 oxidoreductase complex

External links

• PDB: RCSB:1y5i, PDBe:1y5i, PDBj:1y5i
• PDBsum: 1y5i
• PubMed: 15615728
• UniProt: P09152|NARG_ECOLI Respiratory nitrate reductase 1 alpha chain (Gene Name=narG)