Structure of PDB 5cnu Chain D

Receptor sequence

>5cnuD (length=733) Species: 83333 (Escherichia coli K-12)

NLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGI
KTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALY
DHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEG
KYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTF
KISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAG
IGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAAT
LFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDI
TLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMM
QERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVN
DENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAA
KRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLK
ASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALR
ESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILR
QVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSR
FPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRD

3D structure

• PDB: 5cnu Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.
• Chain: D
• Resolution: 3.4 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C225 N437 C439 E441 C462 Y730 Y731
• Catalytic site (residue number reindexed from 1): C222 N434 C436 E438 C459 Y727 Y728
• 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	DGT	D	S249 C292 Q294	S246 C289 Q291
BS02	ADP	D	P208 T209 S224 C225 A252 G253 R298 G299 G300 E441 L464 M620 P621 S622 S625	P205 T206 S221 C222 A249 G250 R295 G296 G297 E438 L461 M617 P618 S619 S622
BS03	DAT	D	V7 K9 R10 E15 I17 N18 K21 V25 T55 H59 F87	V4 K6 R7 E12 I14 N15 K18 V22 T52 H56 F84
BS04	DGT	D	D232 S233 L234 R262 I268 R269 H275 T276	D229 S230 L231 R259 I265 R266 H272 T273

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