Structure of PDB 5cnv Chain D

Receptor sequence

>5cnvD (length=734) Species: 83333 (Escherichia coli K-12)

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

3D structure

• PDB: 5cnv Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.
• Chain: D
• 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): 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	TTP	D	S249 C292	S246 C289
BS02	GDP	D	T209 S224 C225 A252 G253 R298 G299 L438 E441 L464 P621 S622 T624 S625	T206 S221 C222 A249 G250 R295 G296 L435 E438 L461 P618 S619 T621 S622
BS03	DAT	D	V7 K9 R10 N18 K21 V25 T55 H59 K91	V4 K6 R7 N15 K18 V22 T52 H56 K88
BS04	TTP	D	K9 K21 R24 V25 W28 F97	K6 K18 R21 V22 W25 F94
BS05	TTP	D	D232 S233 L234 R262 I268 R269 H275 F281	D229 S230 L231 R259 I265 R266 H272 F278

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)