Structure of PDB 5cnv Chain B

Receptor sequence

>5cnvB (length=732) Species: 83333 (Escherichia coli K-12)

LLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIK
TSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYD
HVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGK
YLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFK
ISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGI
GINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATL
FYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDIT
LFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQ
ERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVND
ENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAK
RGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKA
SNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRE
SIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQ
VVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRF
PSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRD

3D structure

• PDB: 5cnv Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.
• Chain: B
• Resolution: 3.2 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C225 N437 C439 E441 C462 Y730 Y731
• Catalytic site (residue number reindexed from 1): C221 N433 C435 E437 C458 Y726 Y727
• Enzyme Commision number: 1.17.4.1: ribonucleoside-diphosphate reductase.

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	TTP	B	S249 C292	S245 C288
BS02	GDP	B	T209 C225 A252 G253 R298 G299 N437 L438 E441 L464 P621 S622 S625	T205 C221 A248 G249 R294 G295 N433 L434 E437 L460 P617 S618 S621
BS03	DAT	B	V7 K9 R10 E15 N18 K21 V25 T55 H59 K91	V3 K5 R6 E11 N14 K17 V21 T51 H55 K87
BS04	TTP	B	K21 R24 W28 F97	K17 R20 W24 F93
BS05	TTP	B	D232 S233 L234 R262 I268 R269 H275 F281	D228 S229 L230 R258 I264 R265 H271 F277

Gene Ontology

Molecular Function

• GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016491 oxidoreductase activity
• GO:0042802 identical protein binding
• GO:0044183 protein folding chaperone

Biological Process

• GO:0006457 protein folding
• GO:0009185 ribonucleoside diphosphate metabolic process
• GO:0009263 deoxyribonucleotide biosynthetic process
• GO:0009265 2'-deoxyribonucleotide biosynthetic process
• GO:0015949 nucleobase-containing small molecule interconversion

Cellular Component

• GO:0005829 cytosol
• GO:0005971 ribonucleoside-diphosphate reductase complex

External links

• PDB: RCSB:5cnv, PDBe:5cnv, PDBj:5cnv
• PDBsum: 5cnv
• PubMed: 26754917
• UniProt: P00452|RIR1_ECOLI Ribonucleoside-diphosphate reductase 1 subunit alpha (Gene Name=nrdA)