3VPO - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF HUMAN RIBONUCLEOTIDE REDUCTASE SUBUNIT M2 (HRRM2) MUTANT

Authors :   X. Chen, Z. Xu, H. Liu, L. Zhang, B. Chen, L. Zhu, C. Yang, W. Zhu, J. Shao

Date :   05 Mar 12 (Deposition) - 06 Mar 13 (Release) - 06 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Chen, Z. Xu, H. Liu, L. Zhang, B. Chen, L. Zhu, C. Yang, W. Zhu, J. Shao
Essential Role Of E106 In The Proton-Coupled Electron Transfer In Human
To Be Published
PubMed: search

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2
	Chains	:	A, B
	EC Number	:	1.17.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 66-350
	Gene	:	RR2, RRM2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RIBONUCLEOTIDE REDUCTASE SMALL CHAIN, RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT

		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	FE	2	Ligand/Ion	FE (III) ION
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:78 , VAL A:81 , THR A:156 , HOH A:572 , HOH A:583 , HOH A:592	BINDING SITE FOR RESIDUE MG A 401
2	AC2	SOFTWARE	GLN A:165 , GLU A:169 , GLU A:232 , GLU A:266 , HIS A:269	BINDING SITE FOR RESIDUE FE A 402
3	AC3	SOFTWARE	ARG B:78 , VAL B:81 , THR B:156 , HOH B:505 , HOH B:510 , HOH B:566	BINDING SITE FOR RESIDUE MG B 401
4	AC4	SOFTWARE	GLN B:165 , GLU B:169 , GLU B:232 , GLU B:266 , HIS B:269	BINDING SITE FOR RESIDUE FE B 402

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

Asymmetric/Biological Unit

No.	Residues
1	Met A:65	-	Gly A:66
2	Phe A:83	-	Pro A:84
3	Met B:65	-	Gly B:66
4	Phe B:83	-	Pro B:84

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

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_HUMAN	168-184	2	A:168-184 B:168-184

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000304567	1a	ENSE00001406607	chr2:10262455-10263024	570	RIR2_HUMAN	1-33	33	0	-	-
1.1g	ENST00000304567	1g	ENSE00001168586	chr2:10263110-10263184	75	RIR2_HUMAN	34-58	25	0	-	-
1.2c	ENST00000304567	2c	ENSE00001168574	chr2:10263514-10263657	144	RIR2_HUMAN	59-106	48	2	A:65-106 B:65-106	42 42
1.3a	ENST00000304567	3a	ENSE00001168565	chr2:10263863-10263979	117	RIR2_HUMAN	107-145	39	2	A:107-145 B:107-145	39 39
1.4a	ENST00000304567	4a	ENSE00001756022	chr2:10264844-10264977	134	RIR2_HUMAN	146-190	45	2	A:146-190 B:146-190	45 45
1.5e	ENST00000304567	5e	ENSE00001168551	chr2:10267002-10267096	95	RIR2_HUMAN	190-222	33	2	A:190-222 B:190-222	33 33
1.6a	ENST00000304567	6a	ENSE00001168545	chr2:10267214-10267347	134	RIR2_HUMAN	222-266	45	2	A:222-266 B:222-266	45 45
1.7	ENST00000304567	7	ENSE00001168535	chr2:10268975-10269079	105	RIR2_HUMAN	267-301	35	2	A:267-301 B:267-301	35 35
1.8a	ENST00000304567	8a	ENSE00001168527	chr2:10269168-10269281	114	RIR2_HUMAN	302-339	38	2	A:302-339 B:302-339	38 38
1.9b	ENST00000304567	9b	ENSE00001489863	chr2:10269361-10271545	2185	RIR2_HUMAN	340-389	50	2	A:340-350 B:340-350	11 11

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:286
 aligned with RIR2_HUMAN | P31350 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:286
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344      
           RIR2_HUMAN    65 PGVEDEPLLRENPRRFVIFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWESLKPEERYFISHVLAFFAASDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPSEERVREIIINAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFSKVFRVENPFDFM 350
               SCOP domains d3vpoa_ A: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------RIBORED_SMALL    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c  PDB: A:65-106 UniProt: 59-106  Exon 1.3a  PDB: A:107-145              Exon 1.4a  PDB: A:146-190 UniProt: 146-190   -------------------------------Exon 1.6a  PDB: A:222-266 UniProt: 222-266   Exon 1.7  PDB: A:267-301           Exon 1.8a  PDB: A:302-339             Exon 1.9b   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------Exon 1.5e  PDB: A:190-222        -------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3vpo A  65 MGVEDEPLLRENPRRFVIFPIEYHDIWQMYKKAEASFWTAEQVDLSKDIQHWESLKPEERYFISHVLAFFAASDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPSEERVREIIINAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFSKVFRVENPFDFM 350
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with RIR2_HUMAN | P31350 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:286
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344      
           RIR2_HUMAN    65 PGVEDEPLLRENPRRFVIFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWESLKPEERYFISHVLAFFAASDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPSEERVREIIINAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFSKVFRVENPFDFM 350
               SCOP domains d3vpob_ B: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh................hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------RIBORED_SMALL    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c  PDB: B:65-106 UniProt: 59-106  Exon 1.3a  PDB: B:107-145              Exon 1.4a  PDB: B:146-190 UniProt: 146-190   -------------------------------Exon 1.6a  PDB: B:222-266 UniProt: 222-266   Exon 1.7  PDB: B:267-301           Exon 1.8a  PDB: B:302-339             Exon 1.9b   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------Exon 1.5e  PDB: B:190-222        -------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3vpo B  65 MGVEDEPLLRENPRRFVIFPIEYHDIWQMYKKAEASFWTAEQVDLSKDIQHWESLKPEERYFISHVLAFFAASDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPSEERVREIIINAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFSKVFRVENPFDFM 350
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344

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(

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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)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d3vpoa_	A:
1b	d3vpob_	B:

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

(no "Pfam Domain" information available for 3VPO)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RIR2_HUMAN | P31350)

molecular function
	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:0000082	G1/S transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
	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:0009262	deoxyribonucleotide metabolic process	The chemical reactions and pathways involving 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.
	GO:0051290	protein heterotetramerization	The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
	GO:0051259	protein oligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0000083	regulation of transcription involved in G1/S transition of mitotic cell cycle	Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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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	Cis Peptide Bonds
		Met A:65 - Gly A:66	[ RasMol ]
		Met B:65 - Gly B:66	[ RasMol ]
		Phe A:83 - Pro A:84	[ RasMol ]
		Phe B:83 - Pro B:84	[ RasMol ]

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	3vpo
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	RIR2_HUMAN \| P31350
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	1.17.4.1
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	RIR2_HUMAN \| P31350	:	2uw2 3olj 3vpm 3vpn

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (8, 16)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (19, 19)

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