Structure of PDB 2ppa Chain B

Receptor sequence

>2ppaB (length=337) Species: 511 (Alcaligenes faecalis)

ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVID
DAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAAT
GALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGA
IMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAY
EDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTR
PHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAY
VNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT

3D structure

• PDB: 2ppa Conserved active site residues limit inhibition of a copper-containing nitrite reductase by small molecules.
• Chain: B
• Resolution: 1.69 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H95 D98 H100 H135 C136 H145 M150 H255 E279 T280 H306
• Catalytic site (residue number reindexed from 1): H92 D95 H97 H132 C133 H142 M147 H252 E276 T277 H303
• Enzyme Commision number: 1.7.2.1: nitrite reductase (NO-forming).

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	N2O	B	I257 H306	I254 H303
BS02	CU1	B	H95 C136 H145 M150	H92 C133 H142 M147
BS03	CU	B	H100 H135	H97 H132
BS04	ACT	B	G229 I300 H319	G226 I297 H316
BS05	ACT	B	D173 G238	D170 G235
BS06	ACT	B	M141 P143 W144	M138 P140 W141
BS07	N2O	B	H100 H135	H97 H132

Gene Ontology

Molecular Function

• GO:0005507 copper ion binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0050421 nitrite reductase (NO-forming) activity

Biological Process

• GO:0019333 denitrification pathway
• GO:0042128 nitrate assimilation

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:2ppa, PDBe:2ppa, PDBj:2ppa
• PDBsum: 2ppa
• PubMed: 18358002
• UniProt: P38501|NIR_ALCFA Copper-containing nitrite reductase (Gene Name=nirK)