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Title :   RIBONUCLEOTIDE REDUCTASE Y122NO2Y MODIFIED R2 SUBUNIT OF E. COLI

Authors :   K. Yokoyama, U. Uhlin, J. Stubbe

Date :   15 Aug 10 (Deposition) - 25 Aug 10 (Release) - 12 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase, Radical Storage, Dna Replication, Allosteric Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Yokoyama, U. Uhlin, J. Stubbe
A Hot Oxidant, 3-No(2)Y(122) Radical, Unmasks Conformational Gating In Ribonucleotide Reductase.
J. Am. Chem. Soc. V. 132 15368 2010
PubMed-ID: 20929229 | Reference-DOI: 10.1021/JA1069344
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
	Chains	:	A, B
	EC Number	:	1.17.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD-NRDB (Y122Z)
	Expression System Strain	:	TOP10
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	RIBONUCLEOTIDE REDUCTASE 1, PROTEIN B2, PROTEIN R2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FEO	2	Ligand/Ion	MU-OXO-DIIRON
2	NIY	2	Mod. Amino Acid	META-NITRO-TYROSINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:84 , GLU A:115 , HIS A:118 , GLU A:204 , GLU A:238 , HIS A:241 , HOH A:2136 , HOH A:2190	BINDING SITE FOR RESIDUE FEO A 400
2	AC2	SOFTWARE	ASP B:84 , GLU B:115 , HIS B:118 , GLU B:204 , GLU B:238 , HIS B:241 , HOH B:2063 , HOH B:2117	BINDING SITE FOR RESIDUE FEO B 400

(no "SS Bond" information available for 2XOF)

(no "Cis Peptide Bond" information available for 2XOF)

(no "SAP(SNP)/Variant" information available for 2XOF)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBORED_SMALL	PS00368	Ribonucleotide reductase small subunit signature.	RIR2_ECOLI	115-131	2	A:114-130 B:114-130

(no "Exon" information available for 2XOF)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:341
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 
           RIR2_ECOLI     2 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVS 342
               SCOP domains d2xofa_ A: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2xofA00 A:1-341 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh.................hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh............hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xof A   1 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSyTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVS 341
                                    10        20        30        40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
                                                                                                                                                   122-NIY

Chain B from PDB  Type:PROTEIN  Length:341
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 
           RIR2_ECOLI     2 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVS 342
               SCOP domains d2xofb_ B: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2xofB00 B:1-341 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-2xofB01 B:181-335                                                                                                                           ------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-2xofB02 B:181-335                                                                                                                           ------ Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-2xofB03 B:181-335                                                                                                                           ------ Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-2xofB04 B:181-335                                                                                                                           ------ Pfam domains (4)
         Sec.struct. author ..........hhhhh.................hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..............hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xof B   1 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSyTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVS 341
                                    10        20        30        40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
                                                                                                                                                   122-NIY

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Ribonucleotide reductase-like (185)

Protein domain: Ribonucleotide reductase R2 (45)

Escherichia coli [TaxId: 562] (24)

1a	d2xofa_	A:
1b	d2xofb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Ribonucleotide Reductase, subunit A (86)

Homologous Superfamily: Ribonucleotide Reductase, subunit A (86)

Escherichia coli. Organism_taxid: 83333. Strain: k-12. (1)

1a	2xofA00	A:1-341
1b	2xofB00	B:1-341

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ribonuc_red_sm (41)

Escherichia coli (strain K12) (22)

1a	Ribonuc_red_sm-2xofB01	B:181-335
1b	Ribonuc_red_sm-2xofB02	B:181-335
1c	Ribonuc_red_sm-2xofB03	B:181-335
1d	Ribonuc_red_sm-2xofB04	B:181-335

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RIR2_ECOLI | P69924)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004748	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor	Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0009186	deoxyribonucleoside diphosphate metabolic process	The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar.
	GO:0009263	deoxyribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005971	ribonucleoside-diphosphate reductase complex	An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.

Asymmetric/Biological Unit
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1av8	RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FROM E. COLI
1biq	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN MUTANT E238A
1jpr	MN SUBSTITUTED RIBONUCLEOTIDE REDUCTASE R2 FROM E. COLIOXIDIZED BY NITRIC OXIDE
1jqc	MN SUBSTITUTED RIBONUCLEOTIDE REDUCTASE R2 FROM E. COLIOXIDIZED BY HYDROGEN PEROXIDE AND HYDROXYLAMINE
1mrr
1mxr	HIGH RESOLUTION STRUCTURE OF RIBONUCLEOTIDE REDUCTASE R2FROM E. COLI IN ITS OXIDISED (MET) FORM
1pfr	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN
1pim	DITHIONITE REDUCED E. COLI RIBONUCLEOTIDE REDUCTASE R2SUBUNIT, D84E MUTANT
1piu	OXIDIZED RIBONUCLEOTIDE REDUCTASE R2-D84E MUTANT CONTAININGOXO-BRIDGED DIFERRIC CLUSTER
1piy	RIBONUCLEOTIDE REDUCTASE R2 SOAKED WITH FERROUS ION ATNEUTRAL PH
1piz	RIBONUCLEOTIDE REDUCTASE R2 D84E MUTANT SOAKED WITH FERROUSIONS AT NEUTRAL PH
1pj0	RIBONUCLEOTIDE REDUCTASE R2-D84E/W48F MUTANT SOAKED WITHFERROUS IONS AT NEUTRAL PH
1pj1	RIBONUCLEOTIDE REDUCTASE R2-D84E/W48F SOAKED WITH FERROUSIONS AT PH 5
1pm2	CRYSTAL STRUCTURE OF MANGANESE SUBSTITUTED R2 -D84E (D84EMUTANT OF THE R2 SUBUNIT OF E. COLI RIBONUCLEOTIDEREDUCTASE)
1r1r	RIBONUCLEOTIDE REDUCTASE R1 PROTEIN MUTANT Y730F WITH AREDUCED ACTIVE SITE FROM ESCHERICHIA COLI
1r65	CRYSTAL STRUCTURE OF FERROUS SOAKED RIBONUCLEOTIDEREDUCTASE R2 SUBUNIT (WILDTYPE) AT PH 5 FROM E. COLI
1rib
1rnr
1rsr	AZIDE COMPLEX OF THE DIFERROUS F208A MUTANT R2 SUBUNIT OFRIBONUCLEOTIDE REDUCTASE
1rsv	AZIDE COMPLEX OF THE DIFERROUS E238A MUTANT R2 SUBUNIT OFRIBONUCLEOTIDE REDUCTASE
1xik	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN
1yfd	CRYSTAL STRUCTURE OF THE Y122H MUTANT OF RIBONUCLEOTIDEREDUCTASE R2 PROTEIN FROM E. COLI
2alx	RIBONUCLEOTIDE REDUCTASE R2 FROM ESCHERICHIA COLI IN SPACEGROUP P6(1)22
2av8	Y122F MUTANT OF RIBONUCLEOTIDE REDUCTASE FROM ESCHERICHIA COLI
2r1r	RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH DTTP OCCUPYING THESPECIFICITY SITE FROM ESCHERICHIA COLI
2x0x	RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT OF E. COLI TO 2.3 A RESOLUTION
2xak	RIBONUCLEOTIDE REDUCTASE Y730NO2Y MODIFIED R1 SUBUNIT OF E. COLI
2xap	RIBONUCLEOTIDE REDUCTASE Y731NO2Y MODIFIED R1 SUBUNIT OF E. COLI TO 2.1 A RESOLUTION
2xav	RIBONUCLEOTIDE REDUCTASE Y731NO2Y AND Y730F MODIFIED R1 SUBUNIT OF E. COLI
2xaw	RIBONUCLEOTIDE REDUCTASE Y730NO2Y AND Y731F MODIFIED R1 SUBUNIT OF E. COLI
2xax	RIBONUCLEOTIDE REDUCTASE Y730NO2Y AND Y731A MODIFIED R1 SUBUNIT OF E. COLI
2xay	RIBONUCLEOTIDE REDUCTASE Y730NO2Y AND C439A MODIFIED R1 SUBUNIT OF E. COLI
2xaz	RIBONUCLEOTIDE REDUCTASE Y730NO2Y AND C439S MODIFIED R1 SUBUNIT OF E. COLI
2xo4	RIBONUCLEOTIDE REDUCTASE Y730NH2Y MODIFIED R1 SUBUNIT OF E. COLI
2xo5	RIBONUCLEOTIDE REDUCTASE Y731NH2Y MODIFIED R1 SUBUNIT OF E. COLI
3r1r	RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH AMPPNP OCCUPYINGTHE ACTIVITY SITE FROM ESCHERICHIA COLI
4r1r	RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH SUBSTRATE, GDP ANDEFFECTOR DTTP FROM ESCHERICHIA COLI
5r1r	RIBONUCLEOTIDE REDUCTASE E441A MUTANT R1 PROTEIN FROMESCHERICHIA COLI
6r1r	RIBONUCLEOTIDE REDUCTASE E441D MUTANT R1 PROTEIN FROMESCHERICHIA COLI
7r1r	RIBONUCLEOTIDE REDUCTASE E441Q MUTANT R1 PROTEIN FROMESCHERICHIA COLI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 4)

Gene Ontology (13, 13)

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