Structure of PDB 4erm Chain C

Receptor sequence

>4ermC (length=731) Species: 83333 (Escherichia coli K-12)

VTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTS
DIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHV
VKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYL
VQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKIS
LPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGI
NAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFY
PMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLF
SPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQER
ASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDEN
GEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRG
AMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASN
ELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESI
KTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVV
PDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPS
GKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG

3D structure

• PDB: 4erm Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.
• Chain: C
• Resolution: 3.95 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C225 N437 C439 E441 C462 Y730 Y731
• Catalytic site (residue number reindexed from 1): C219 N431 C433 E435 C456 Y724 Y725
• 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	DTP	C	K9 R10 E15 I17 N18 I22 V25 T55 H59	K3 R4 E9 I11 N12 I16 V19 T49 H53
BS02	DAT	C	P208 T209 C225 N437 L438 C439 E441 L464 P621 S625	P202 T203 C219 N431 L432 C433 E435 L458 P615 S619
BS03	DTP	C	D232 S233 L234 R262 I268 R269 H275 T276	D226 S227 L228 R256 I262 R263 H269 T270
BS04	DTP	C	S249 C292	S243 C286

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:4erm, PDBe:4erm, PDBj:4erm
• PDBsum: 4erm
• PubMed: 22727814
• UniProt: P00452|RIR1_ECOLI Ribonucleoside-diphosphate reductase 1 subunit alpha (Gene Name=nrdA)