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Title :   RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI IN COMPLEX WITH REDUCED NRDI WITH A TRAPPED PEROXIDE

Authors :   A. K. Boal, J. A. Cotruvo Jr. , J. Stubbe, A. C. Rosenzweig

Date :   19 May 10 (Deposition) - 18 Aug 10 (Release) - 24 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.36

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

Keywords :   Ribonucleotide Reductase, Four-Helix Bundle, Dimanganese Cluster, Flavoprotein, Peroxide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Boal, J. A. Cotruvo, J. Stubbe, A. C. Rosenzweig
Structural Basis For Activation Of Class Ib Ribonucleotide Reductase.
Science V. 329 1526 2010
PubMed-ID: 20688982 | Reference-DOI: 10.1126/SCIENCE.1190187

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 SUBUNIT BETA
	Chains	:	B, A
	EC Number	:	1.17.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	B2676, JW2651, NRDF, YGAD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	RIBONUCLEOTIDE REDUCTASE 2, R2F PROTEIN

Molecule 2 - PROTEIN NRDI
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NRDI, YGAO, B2674, JW2649
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MN	4	Ligand/Ion	MANGANESE (II) ION
3	PEO	2	Ligand/Ion	HYDROGEN PEROXIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:67 , GLU B:98 , HIS B:101 , GLU B:158 , GLU B:192 , MN B:321 , HOH B:375	BINDING SITE FOR RESIDUE MN B 320
2	AC2	SOFTWARE	GLU B:98 , GLU B:158 , GLU B:192 , HIS B:195 , MN B:320 , HOH B:381	BINDING SITE FOR RESIDUE MN B 321
3	AC3	SOFTWARE	SER B:159 , LYS B:260 , HOH B:329 , ASN C:83 , ASN C:85	BINDING SITE FOR RESIDUE PEO B 322
4	AC4	SOFTWARE	ARG B:25 , TYR B:197 , SER C:8 , SER C:9 , SER C:11 , GLU C:12 , ASN C:13 , THR C:14 , PRO C:47 , SER C:48 , TYR C:49 , GLY C:50 , GLY C:51 , GLY C:82 , ASN C:83 , PHE C:86 , ALA C:89 , TYR C:90 , GLY C:91 , LEU C:111 , HOH C:138 , HOH C:143	BINDING SITE FOR RESIDUE FMN C 134
5	AC5	SOFTWARE	ASP A:67 , GLU A:98 , HIS A:101 , GLU A:158 , GLU A:192 , HOH A:361	BINDING SITE FOR RESIDUE MN A 320
6	AC6	SOFTWARE	GLU A:98 , GLU A:158 , GLU A:192 , HIS A:195 , HOH A:334	BINDING SITE FOR RESIDUE MN A 321
7	AC7	SOFTWARE	SER A:159 , LYS A:260 , ASN A:264 , HOH A:359 , ASN D:83 , ASN D:85	BINDING SITE FOR RESIDUE PEO A 322
8	AC8	SOFTWARE	ARG A:25 , TYR A:197 , SER D:8 , SER D:9 , SER D:11 , GLU D:12 , ASN D:13 , THR D:14 , PRO D:47 , SER D:48 , TYR D:49 , GLY D:50 , SER D:81 , GLY D:82 , ASN D:83 , PHE D:86 , ALA D:89 , TYR D:90 , GLY D:91 , LEU D:111 , HOH D:136	BINDING SITE FOR RESIDUE FMN D 134

(no "SS Bond" information available for 3N3B)

(no "Cis Peptide Bond" information available for 3N3B)

(no "SAP(SNP)/Variant" information available for 3N3B)

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.	RIR4_ECOLI	97-113	2	A:97-113 B:97-113

(no "Exon" information available for 3N3B)

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:284
 aligned with RIR4_ECOLI | P37146 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:284
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
           RIR4_ECOLI     5 RISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
               SCOP domains d3n3ba_ A: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3b A   5 RISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284

Chain B from PDB  Type:PROTEIN  Length:284
 aligned with RIR4_ECOLI | P37146 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:284
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
           RIR4_ECOLI     5 RISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
               SCOP domains d3n3bb_ B: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Ribonuc_red_sm-3n3bB01 B:5-281                                                                                                                                                                                                                                                       ------- Pfam domains (1)
           Pfam domains (2) Ribonuc_red_sm-3n3bB02 B:5-281                                                                                                                                                                                                                                                       ------- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3b B   5 RISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with NRDI_ECOLI | P0A772 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:129
                                    12        22        32        42        52        62        72        82        92       102       112       122         
           NRDI_ECOLI     3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQR 131
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....hhhhhhhhhhh..eee..............eeeeee...........hhhhhhhhhhhhhhh.eeeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3b C   3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQR 131
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with NRDI_ECOLI | P0A772 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:129
                                    12        22        32        42        52        62        72        82        92       102       112       122         
           NRDI_ECOLI     3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQR 131
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Flavodoxin_NdrI-3n3bD01 D:5-123                                                                                        -------- Pfam domains (1)
           Pfam domains (2) --Flavodoxin_NdrI-3n3bD02 D:5-123                                                                                        -------- Pfam domains (2)
         Sec.struct. author .eeee....hhhhhhhhhhh..eeee.............eeeeee...........hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3b D   3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQR 131
                                    12        22        32        42        52        62        72        82        92       102       112       122

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: automated matches (42)

Escherichia coli K-12 [TaxId: 83333] (6)

1a	d3n3ba_	A:
1b	d3n3bb_	B:

(no "CATH Domain" information available for 3N3B)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ribonuc_red_sm (41)

Escherichia coli (strain K12) (22)

1a	Ribonuc_red_sm-3n3bB01	B:5-281
1b	Ribonuc_red_sm-3n3bB02	B:5-281

Clan: Flavoprotein (71)

Family: Flavodoxin_NdrI (8)

Escherichia coli (strain K12) (3)

2a	Flavodoxin_NdrI-3n3bD01	D:5-123
2b	Flavodoxin_NdrI-3n3bD02	D:5-123

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RIR4_ECOLI | P37146)

molecular function
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) 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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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: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: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.

Chain C,D (NRDI_ECOLI | P0A772)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3n3b)

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	RIR4_ECOLI \| P37146
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	1.17.4.1
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UniProtKB/Swiss-Prot
	NRDI_ECOLI \| P0A772	:	3n39 3n3a
	RIR4_ECOLI \| P37146	:	3n37 3n38 3n39 3n3a 4m1f

3n37	RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI
3n38	RIBONUCLEOTIDE REDUCTASE NRDF FROM ESCHERICHIA COLI SOAKED WITH FERROUS IONS
3n39	RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI IN COMPLEX WITH NRDI
3n3a	RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI IN COMPLEX WITH REDUCED NRDI

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (14, 15)

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