3N39 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

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

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 :   2.50

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

Keywords :   Ribonucleotide Reductase, Four-Helix Bundle, Dimanganese Cluster, Flavoprotein, 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 (2, 6)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:67 , GLU B:98 , HIS B:101 , GLU B:158 , GLU B:192 , HOH B:323	BINDING SITE FOR RESIDUE MN B 320
2	AC2	SOFTWARE	GLU B:98 , GLU B:158 , GLU B:192 , HIS B:195 , HOH B:322	BINDING SITE FOR RESIDUE MN B 321
3	AC3	SOFTWARE	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:135	BINDING SITE FOR RESIDUE FMN C 134
4	AC4	SOFTWARE	GLU A:98 , GLU A:158 , GLU A:192 , HIS A:195 , MN A:321 , HOH A:323	BINDING SITE FOR RESIDUE MN A 320
5	AC5	SOFTWARE	ASP A:67 , GLU A:98 , HIS A:101 , GLU A:158 , GLU A:192 , MN A:320 , HOH A:322	BINDING SITE FOR RESIDUE MN A 321
6	AC6	SOFTWARE	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 , GLY D:51 , GLY D:82 , ASN D:83 , PHE D:86 , ALA D:89 , TYR D:90 , GLY D:91 , LEU D:111 , HOH D:135	BINDING SITE FOR RESIDUE FMN D 134

(no "SS Bond" information available for 3N39)

(no "Cis Peptide Bond" information available for 3N39)

(no "SAP(SNP)/Variant" information available for 3N39)

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 3N39)

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:282
 aligned with RIR4_ECOLI | P37146 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:282
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  
           RIR4_ECOLI     7 SAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
               SCOP domains d3n39a_ A: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n39 A   7 SAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with RIR4_ECOLI | P37146 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:282
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
           RIR4_ECOLI     6 ISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALS 287
               SCOP domains d3n39b_ B: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Ribonuc_red_sm-3n39B01 B:6-281                                                                                                                                                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) Ribonuc_red_sm-3n39B02 B:6-281                                                                                                                                                                                                                                                      ------ Pfam domains (2)
         Sec.struct. author ..........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n39 B   6 ISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALS 287
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285

Chain C from PDB  Type:PROTEIN  Length:128
 aligned with NRDI_ECOLI | P0A772 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:128
                                    12        22        32        42        52        62        72        82        92       102       112       122        
           NRDI_ECOLI     3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQ 130
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....hhhhhhhhh....eee..............eeeeee...........hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n39 C   3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQ 130
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain D from PDB  Type:PROTEIN  Length:128
 aligned with NRDI_ECOLI | P0A772 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:128
                                    12        22        32        42        52        62        72        82        92       102       112       122        
           NRDI_ECOLI     3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQ 130
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Flavodoxin_NdrI-3n39D01 D:5-123                                                                                        ------- Pfam domains (1)
           Pfam domains (2) --Flavodoxin_NdrI-3n39D02 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
                 3n39 D   3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQ 130
                                    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	d3n39a_	A:
1b	d3n39b_	B:

(no "CATH Domain" information available for 3N39)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ribonuc_red_sm (41)

Escherichia coli (strain K12) (22)

1a	Ribonuc_red_sm-3n39B01	B:6-281
1b	Ribonuc_red_sm-3n39B02	B:6-281

Clan: Flavoprotein (71)

Family: Flavodoxin_NdrI (8)

Escherichia coli (strain K12) (3)

2a	Flavodoxin_NdrI-3n39D01	D:5-123
2b	Flavodoxin_NdrI-3n39D02	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 3n39)

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	3n39
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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	:	3n3a 3n3b
	RIR4_ECOLI \| P37146	:	3n37 3n38 3n3a 3n3b 4m1f

3n37	RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI
3n38	RIBONUCLEOTIDE REDUCTASE NRDF FROM ESCHERICHIA COLI SOAKED WITH FERROUS IONS
3n3a	RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI IN COMPLEX WITH REDUCED NRDI
3n3b	STRUCTURAL BASIS FOR ACTIVATION OF CLASS IB RIBONUCLEOTIDE REDUCTASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (14, 15)

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