2OIG - JenaLib

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Title :   CRYSTAL STRUCTURE OF RS21-C6 CORE SEGMENT AND DM5CTP COMPLEX

Authors :   B. Wu, Y. Liu, Q. Zhao, S. Liao, J. Zhang, M. Bartlam, W. Chen, Z. Rao

Date :   11 Jan 07 (Deposition) - 06 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Helix, Protein-Nucleoside Triphosphate Complex, Substrate Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Wu, Y. Liu, Q. Zhao, S. Liao, J. Zhang, M. Bartlam, W. Chen, Z. Rao
Crystal Structure Of Rs21-C6, Involved In Nucleoside Triphosphate Pyrophosphohydrolysis
J. Mol. Biol. V. 367 1405 2007
PubMed-ID: 17320107 | Reference-DOI: 10.1016/J.JMB.2007.01.057
(for further references see the PDB file header)

Molecule 1 - RS21-C6
	Cdna, Riken Full-length Enriched Library, Clone	:	1110012M04
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CORE SEGMENT, RESIDUES 21-126
	Full-length Enriched Library, Clone	:	2410029L09
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Product	:	RS21-C6 HOMOLOG, ES CELLS CDNA, RIKEN FULL-LENGTH ENRICHED LIBRARY, CLONE:2410015N17 PRODUCT:HYPOTHETICAL PROTEIN, FULL INSERT SEQUENCE, 18-DAY EMBRYO WHOLE BODY; RS21-C6 2410015N17RIK PROTEIN, RIKEN CDNA 2410015N17 GENE, FULL INSERT SEQUENCE, RSCUT
	Synonym	:	RIKEN CDNA 2410015N17 GENE, ES CELLS CDNA, RIKEN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	523	2	Ligand/Ion	2'-DEOXY-5-METHYLCYTIDINE 5'-(TETRAHYDROGENTRIPHOSPHATE)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:47 , GLU A:63 , GLU A:66 , ASP A:98 , ILE A:101 , TYR A:102 , HOH A:127 , HOH A:176 , GLU D:69 , TRP D:73 , HOH D:899 , HOH D:908 , HOH D:929	BINDING SITE FOR RESIDUE 523 D 888
2	AC2	SOFTWARE	HIS B:38 , TRP B:47 , PHE B:50 , HIS B:51 , GLU B:63 , GLU B:66 , ILE B:101 , TYR B:102 , HOH B:1893 , HOH B:1930 , HOH B:1936 , HOH B:1943 , HOH B:1949 , HOH B:1955 , TRP C:73	BINDING SITE FOR RESIDUE 523 B 1888

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:28	-	Pro A:29
2	Glu B:28	-	Pro B:29
3	Glu C:28	-	Pro C:29
4	Glu D:28	-	Pro D:29

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EAR	PS50912	EAR repeat profile.	DCTP1_MOUSE	29-75	4	A:29-75 B:29-75 C:29-75 D:29-75

(no "Exon" information available for 2OIG)

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:104
 aligned with DCTP1_MOUSE | Q9QY93 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:104
                                    31        41        51        61        71        81        91       101       111       121    
          DCTP1_MOUSE    22 PFRFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKSDTEPGPQAWPPKERAALQEELSDVLIYLVALAARCHVDLPQAVISKMDTN 125
               SCOP domains d2oiga1 A:22-125 XTP3-transactivated gene A protein homolog RS21-C6                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------EAR  PDB: A:29-75 UniProt: 29-75               -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2oig A  22 PFRFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKSDTEPGPQAWPPKERAALQEELSDVLIYLVALAARCHVDLPQAVISKMDTN 125
                                    31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with DCTP1_MOUSE | Q9QY93 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:102
                                    30        40        50        60        70        80        90       100       110       120  
          DCTP1_MOUSE    21 RPFRFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKSDTEPGPQAWPPKERAALQEELSDVLIYLVALAARCHVDLPQAVISKM 122
               SCOP domains d2oigb1 B:21-122 XTP3-transactivated gene A protein homolog RS21-C6                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------EAR  PDB: B:29-75 UniProt: 29-75               ----------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2oig B  21 RPFRFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKSDTEPGPQAWPPKERAALQEELSDVLIYLVALAARCHVDLPQAVISKM 122
                                    30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:90
 aligned with DCTP1_MOUSE | Q9QY93 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:101
                                    31        41        51        61        71        81        91       101       111       121 
          DCTP1_MOUSE    22 PFRFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKSDTEPGPQAWPPKERAALQEELSDVLIYLVALAARCHVDLPQAVISKM 122
               SCOP domains d2oigc1 C:22-122 X         TP3-transactivated gene A pro  tein homolog RS21-C6                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh---------...hhhhhhhhhhhhhhhhhhh.......--hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------EAR  PDB: C:29-75 UniProt: 29-75               ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2oig C  22 PFRFSPEPTLEDIRRLHA---------QFHQPRNLLLALVGEVGELAELFQWKSDT--GPQAWPPKERAALQEELSDVLIYLVALAARCHVDLPQAVISKM 122
                                    31       | -       |51        61        71     |  81        91       101       111       121 
                                            39        49                          77 80

Chain D from PDB  Type:PROTEIN  Length:104
 aligned with DCTP1_MOUSE | Q9QY93 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:104
                                    30        40        50        60        70        80        90       100       110       120    
          DCTP1_MOUSE    21 RPFRFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKSDTEPGPQAWPPKERAALQEELSDVLIYLVALAARCHVDLPQAVISKMDT 124
               SCOP domains d2oigd1 D:21-124 XTP3-transactivated gene A protein homolog RS21-C6                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------MazG-2oigD01 D:51-124                                                      Pfam domains (1)
           Pfam domains (2) ------------------------------MazG-2oigD02 D:51-124                                                      Pfam domains (2)
           Pfam domains (3) ------------------------------MazG-2oigD03 D:51-124                                                      Pfam domains (3)
           Pfam domains (4) ------------------------------MazG-2oigD04 D:51-124                                                      Pfam domains (4)
         Sec.struct. author .........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------EAR  PDB: D:29-75 UniProt: 29-75               ------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2oig D  21 RPFRFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKSDTEPGPQAWPPKERAALQEELSDVLIYLVALAARCHVDLPQAVISKMDT 124
                                    30        40        50        60        70        80        90       100       110       120

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: all-alpha NTP pyrophosphatases (26)

Superfamily: all-alpha NTP pyrophosphatases (26)

Family: MazG-like (6)

Protein domain: XTP3-transactivated gene A protein homolog RS21-C6 (4)

Mouse (Mus musculus) [TaxId: 10090] (4)

1a	d2oiga1	A:22-125
1b	d2oigc1	C:22-122
1c	d2oigd1	D:21-124
1d	d2oigb1	B:21-122

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MazG (25)

Family: MazG (9)

Mus musculus (Mouse) (3)

1a	MazG-2oigD01	D:51-124
1b	MazG-2oigD02	D:51-124
1c	MazG-2oigD03	D:51-124
1d	MazG-2oigD04	D:51-124

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (DCTP1_MOUSE | Q9QY93)

molecular function
	GO:0047840	dCTP diphosphatase activity	Catalysis of the reaction: dCTP + H2O = dCMP + diphosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0047429	nucleoside-triphosphate diphosphatase activity	Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide.
	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:0032556	pyrimidine deoxyribonucleotide binding	Interacting selectively and non-covalently with a pyrimidine deoxyribonucleotide, any compound consisting of a pyrimidine deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety.
	GO:0016462	pyrophosphatase activity	Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments.
biological process
	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:0009143	nucleoside triphosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:28 - Pro A:29	[ RasMol ]
		Glu B:28 - Pro B:29	[ RasMol ]
		Glu C:28 - Pro C:29	[ RasMol ]
		Glu D:28 - Pro D:29	[ RasMol ]

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	2oig
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	DCTP1_MOUSE \| Q9QY93	:	2a3q 2oie 2q4p

2oie	THE SAME PROTEIN WITHOUT LIGANDS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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Gene Ontology (14, 14)

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