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Title :   STRUCTURES OF YEAST RIBONUCLEOTIDE REDUCTASE I COMPLEXED WITH LIGANDS AND SUBUNIT PEPTIDES

Authors :   C. Dealwis, H. Xu, C. Faber, T. Uchiki, J. W. Fairman, J. Racca

Date :   28 Oct 05 (Deposition) - 07 Mar 06 (Release) - 17 Feb 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Ribonucleotide Reductase, Ligand Interaction, Subunit Assembly, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Xu, C. Faber, T. Uchiki, J. Racca, C. Dealwis
Structures Of Eukaryotic Ribonucleotide Reductase I Define Gemcitabine Diphosphate Binding And Subunit Assembly.
Proc. Natl. Acad. Sci. Usa V. 103 4028 2006
PubMed-ID: 16537480 | Reference-DOI: 10.1073/PNAS.0600440103

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN 1
	Chains	:	A
	EC Number	:	1.17.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PWJ751-2
	Expression System Strain	:	BL21(DE3)PLYS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RNR1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	RIBONUCLEOTIDE REDUCTASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	GCQ	1	Ligand/Ion	GEMCITABINE DIPHOSPHATE
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	GCQ	2	Ligand/Ion	GEMCITABINE DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ANP A:890	BINDING SITE FOR RESIDUE MG A 889
2	AC2	SOFTWARE	ASP A:226 , SER A:227 , ILE A:228 , ILE A:231 , LYS A:243 , ARG A:256 , ILE A:262 , ALA A:263 , TYR A:285 , VAL A:286 , ASP A:287 , GLN A:288 , GLY A:289 , MG A:889 , HOH A:916 , HOH A:927 , HOH A:935 , HOH A:958 , HOH A:1091	BINDING SITE FOR RESIDUE ANP A 890
3	AC3	SOFTWARE	ALA A:201 , SER A:202 , PHE A:206 , SER A:217 , CYS A:218 , GLY A:246 , GLY A:247 , ARG A:293 , LEU A:427 , CYS A:428 , MET A:606 , PRO A:607 , THR A:608 , ALA A:609 , SER A:610 , THR A:611 , HOH A:1024 , HOH A:1060 , HOH A:1089	BINDING SITE FOR RESIDUE GCQ A 891

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

Asymmetric Unit

No.	Residues
1	Thr A:401	-	Pro A:402

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_YEAST	585-607	1	A:585-607

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_YEAST	585-607	2	A:585-607

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YER070W	1	YER070W.1	V:298948-301614	2667	RIR1_YEAST	1-888	888	1	A:90-746 (gaps)	657

Asymmetric 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:648
 aligned with RIR1_YEAST | P21524 from UniProtKB/Swiss-Prot  Length:888

    Alignment length:657
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       
           RIR1_YEAST    90 TTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYSRRVLSGEFQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh..ee..ee..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eeehhhhhhhh.........eeeee....hhhhhhhhhhhhhhhhh...eeeee...................hhhhhhhhhhhhhhhh..........eeeee.....hhhhhh...............eeeeeeehhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh..eeeehhhhhhh...........................ee..eeeee....ee........eehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhh.......hhhhhhhhhhhhh.............hhhhhhh............---------....hhhhhhhhhh.......hhhhhhhh..........hhhhhhhh......hhhhhhhhhhhhhh.........eee...hhhhhhhhhhhhhhh...eee..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:90-746 (gaps) UniProt: 1-888 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Transcript 1
                 2eud A  90 TTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNM---------FQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619        |-       639       649       659       669       679       689       699       709       719       729       739       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    628       638

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 '\|'

(no "SCOP Domain" information available for 2EUD)

(no "CATH Domain" information available for 2EUD)

(no "Pfam Domain" information available for 2EUD)

Asymmetric Unit(hide GO term definitions)

Chain A (RIR1_YEAST | P21524)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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: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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.

Asymmetric Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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