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Title :   STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP

Authors :   K. -M. Larsson, J. Andersson, B. -M. Sjoeberg, P. Nordlund, D. T. Logan

Date :   06 Mar 03 (Deposition) - 27 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Oxidoreductase, Reductase, Allosteric Regulation, Substrate Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. T. Logan, E. Mulliez, K. -M. Larsson, S. Bodevin, M. Atta, P. E. Garnaud, B. -M. Sjoberg, M. Fontecave
A Metal-Binding Site In The Catalytic Subunit Of Anaerobic Ribonucleotide Reductase.
Proc. Natl. Acad. Sci. Usa V. 100 3826 2003
PubMed-ID: 12655046 | Reference-DOI: 10.1073/PNAS.0736456100
(for further references see the PDB file header)

Molecule 1 - ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE
	Chains	:	A
	EC Number	:	1.17.4.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET29T4NRDD(G580A)
	Expression System Strain	:	JM109(DE3)
	Expression System Taxid	:	562
	Fragment	:	ACTIVE SITE SUBUNIT, RESIDUES 1-605
	Mutation	:	YES
	Organism Scientific	:	BACTERIOPHAGE T4
	Organism Taxid	:	10665
	Other Details	:	SEQUENCE DETERMINATION: P.YOUNG, M.OHMAN, M.Q.XU.

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	DGT	2	Ligand/Ion	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2	MN	1	Ligand/Ion	MANGANESE (II) ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	DGT	4	Ligand/Ion	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:543 , CYS A:546 , CYS A:561 , CYS A:564	BINDING SITE FOR RESIDUE ZN A1589
2	AC2	SOFTWARE	DGT A:1587	BINDING SITE FOR RESIDUE MN A1590
3	AC3	SOFTWARE	GLU A:100 , PRO A:102 , LYS A:103 , VAL A:107 , ILE A:111 , LYS A:146 , LYS A:169 , ASP A:173 , GLN A:176 , ALA A:177 , TYR A:180 , GLU A:181 , MN A:1590 , HOH A:2077 , HOH A:2220 , HOH A:2221 , HOH A:2222 , HOH A:2223	BINDING SITE FOR RESIDUE DGT A1587
4	AC4	SOFTWARE	HIS A:64 , HIS A:66 , ASP A:67 , GLU A:446 , ASN A:447 , LEU A:448 , HOH A:2014 , HOH A:2224 , HOH A:2226 , HOH A:2227 , HOH A:2228	BINDING SITE FOR RESIDUE DGT A1588

(no "SS Bond" information available for 1HK8)

Asymmetric Unit

No.	Residues
1	Ser A:71	-	Pro A:72
2	Phe A:231	-	Pro A:232
3	Tyr A:266	-	Pro A:267

(no "SAP(SNP)/Variant" information available for 1HK8)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLY_RADICAL_2	PS51149	Glycine radical domain profile.	NRDD_BPT4	482-605	1	A:482-586
2	GLY_RADICAL_1	PS00850	Glycine radical domain signature.	NRDD_BPT4	575-583	1	A:575-583

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLY_RADICAL_2	PS51149	Glycine radical domain profile.	NRDD_BPT4	482-605	2	A:482-586
2	GLY_RADICAL_1	PS00850	Glycine radical domain signature.	NRDD_BPT4	575-583	2	A:575-583

(no "Exon" information available for 1HK8)

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:561
 aligned with NRDD_BPT4 | P07071 from UniProtKB/Swiss-Prot  Length:605

    Alignment length:561
                                    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       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585 
            NRDD_BPT4    26 DSRVFPTQRDLMAGIVSKHIAKNMVPSFIMKAHESGIIHVHDIDYSPALPFTNCCLVDLKGMLENGFKLGNAQIETPKSIGVATAIMAQITAQVASHQYGGTTFANVDKVLSPYVKRTYAKHIEDAEKWQIADALNYAQSKTEKDVYDAFQAYEYEVNTLFSSNGQTPFVTITFGTGTDWTERMIQKAILKNRIKGLGRDGITPIFPKLVMFVEEGVNLYKDDPNYDIKQLALECASKRMYPDIISAKNNKAITGSSVPVSPMGCRSFLSVWKDSTGNEILDGRNNLGVVTLNLPRIALDSYIGTQFNEQKFVELFNERMDLCFEALMCRISSLKGVKATVAPILYQEGAFGVRLKPDDDIIELFKNGRSSVSLGYIGIHELNILVGRDIGREILTKMNAHLKQWTERTGFAFSLYSTPAENLCYRFCKLDTEKYGSVKDVTDKGWYTNSFHVSVEENITPFEKISREAPYHFIATGGHISYVELPDMKNNLKGLEAVWDYAAQHLDYFGVNMPVDKCFTCGSTHEMTPTENGFVCSICGETDPKKMNTIRRTCGYLGNPN 586
               SCOP domains d1hk8a_ A: Class III anaerobic ribonucleotide reductase NRDD subunit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1hk8A00 A:26-586  [code=3.20.70.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..............ee.hhhhhhhh.eee..eee....hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee....hhhhhhhhhhhhhhhhhh...........eeeeee...........hhhhhhhhhhhhhhhh..eeeehhhhhhhhh..............................eeeeeeeehhhhhhh.ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.............hhhhhh....eeeeeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhh.......eeee......hhhhhhhhhhhhhhhh.eeeee..eeee.........ee....ee.......hhh.eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLY_RADICAL_2  PDB: A:482-586 UniProt: 482-605                                                            PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLY_RADIC--- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hk8 A  26 DSRVFPTQRDLMAGIVSKHIAKNMVPSFIMKAHESGIIHVHDIDYSPALPFTNCCLVDLKGMLENGFKLGNAQIETPKSIGVATAIMAQITAQVASHQYGGTTFANVDKVLSPYVKRTYAKHIEDAEKWQIADALNYAQSKTEKDVYDAFQAYEYEVNTLFSSNGQTPFVTITFGTGTDWTERMIQKAILKNRIKGLGRDGITPIFPKLVMFVEEGVNLYKDDPNYDIKQLALECASKRMYPDIISAKNNKAITGSSVPVSPMGCRSFLSVWKDSTGNEILDGRNNLGVVTLNLPRIALDSYIGTQFNEQKFVELFNERMDLCFEALMCRISSLKGVKATVAPILYQEGAFGVRLKPDDDIIELFKNGRSSVSLGYIGIHELNILVGRDIGREILTKMNAHLKQWTERTGFAFSLYSTPAENLCYRFCKLDTEKYGSVKDVTDKGWYTNSFHVSVEENITPFEKISREAPYHFIATGGHISYVELPDMKNNLKGLEAVWDYAAQHLDYFGVNMPVDKCFTCGSTHEMTPTENGFVCSICGETDPKKMNTIRRTCAYLGNPN 586
                                    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       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: Anaerobic Ribonucleotide-triphosphate Reductase Large Chain (15)

Homologous Superfamily: [code=3.20.70.20, no name defined] (15)

Bacteriophage t4. Organism_taxid: 10665. (3)

1hk8A00

A:26-586

(no "Pfam Domain" information available for 1HK8)

Asymmetric Unit(hide GO term definitions)

Chain A (NRDD_BPT4 | P07071)

molecular function
	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: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:0008998	ribonucleoside-triphosphate reductase activity	Catalysis of the reaction: 2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H2O = ribonucleoside triphosphate + 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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:231 - Pro A:232	[ RasMol ]
		Ser A:71 - Pro A:72	[ RasMol ]
		Tyr A:266 - Pro A:267	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1hk8
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	NRDD_BPT4 \| P07071
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	1.17.4.2
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UniProtKB/Swiss-Prot
	NRDD_BPT4 \| P07071	:	1h78 1h79 1h7a 1h7b

1h78	STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DCTP.
1h79	STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DTTP
1h7a	STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DATP.
1h7b	STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NATIVE NRDD

Description

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Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (7, 7)

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