Structure of PDB 5cnv Chain A

Receptor sequence

>5cnvA (length=736) Species: 83333 (Escherichia coli K-12)

MNQNLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFY
DGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPP
ALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQ
LEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAV
STFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQ
RAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGG
AATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKG
EDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFS
LMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLN
DVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPI
PAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYY
LLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWE
ALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDG
ILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYD
PSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRD

3D structure

• PDB: 5cnv Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.
• Chain: A
• 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): C225 N437 C439 E441 C462 Y730 Y731
• 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	GDP	A	T209 S224 C225 G253 R298 G299 L438 E441 L464 P621 S622 T624 S625	T209 S224 C225 G253 R298 G299 L438 E441 L464 P621 S622 T624 S625
BS02	DAT	A	V7 K9 R10 E15 N18 K21 V25 T55 H59 K91	V7 K9 R10 E15 N18 K21 V25 T55 H59 K91
BS03	TTP	A	K9 K21 R24 W28 F97	K9 K21 R24 W28 F97
BS04	TTP	A	D232 S233 L234 R262 I268 R269 H275 F281	D232 S233 L234 R262 I268 R269 H275 F281
BS05	TTP	A	S249 C292	S249 C292

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)