2O5F - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DR0079 FROM DEINOCOCCUS RADIODURANS AT 1.9 ANGSTROM RESOLUTION

Authors :   M. A. Kennedy, G. W. Buchko, S. Ni, H. Robinson

Date :   05 Dec 06 (Deposition) - 18 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Alpha Plus Beta, Nudix Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. W. Buchko, O. Litvinova, H. Robinson, A. F. Yakunin, M. A. Kennedy
Functional And Structural Characterization Of Dr_0079 From Deinococcus Radiodurans, A Novel Nudix Hydrolase With A Preference For Cytosine (Deoxy)Ribonucleoside 5'-Di- And Triphosphates.
Biochemistry V. 47 6571 2008
PubMed-ID: 18512963 | Reference-DOI: 10.1021/BI800099D

Molecule 1 - PUTATIVE NUDIX HYDROLASE DR_0079
	Chains	:	A, B
	EC Number	:	3.6.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30B
	Expression System Strain	:	K12 BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DR0079
	Organism Scientific	:	DEINOCOCCUS RADIODURANS
	Organism Taxid	:	243230
	Strain	:	R1

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2O5F)

(no "Site" information available for 2O5F)

(no "SS Bond" information available for 2O5F)

(no "Cis Peptide Bond" information available for 2O5F)

(no "SAP(SNP)/Variant" information available for 2O5F)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	Y079_DEIRA	32-162	2	A:32-162 B:32-162
2	NUDIX_BOX	PS00893	Nudix box signature.	Y079_DEIRA	70-91	2	A:70-91 B:70-91

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	Y079_DEIRA	32-162	1	A:32-162 -
2	NUDIX_BOX	PS00893	Nudix box signature.	Y079_DEIRA	70-91	1	A:70-91 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	Y079_DEIRA	32-162	1	- B:32-162
2	NUDIX_BOX	PS00893	Nudix box signature.	Y079_DEIRA	70-91	1	- B:70-91

(no "Exon" information available for 2O5F)

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:155
 aligned with Y079_DEIRA | Q9RY71 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:162
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166  
           Y079_DEIRA     7 ERLDLVNERDEVVGQILRTDPALRWERVRVVNAFLRNSQGQLWIPRRSPSKSLFPNALDVSVGGAVQSGETYEEAFRREAREELNVEIDALSWRPLASFSPFQTTLSSFMCVYELRSDATPIFNPNDISGGEWLTPEHLLARIAAGEAAKGDLAELVRRCYR 168
               SCOP domains d2o5fa_ A: Hypothetical protein DR0079                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeeee......hhhh.eeeeeeee.....eeeee.-------.......eeee.....hhhhhhhhhhhhhhh.hhhhheeeeeeee.........eeeeeeee.............eeeeehhhhhhhhhhhh.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------NUDIX  PDB: A:32-162 UniProt: 32-162                                                                                               ------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------NUDIX_BOX  PDB: A:70-9----------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o5f A   7 ERLDLVNERDEVVGQILRTDPALRWERVRVVNAFLRNSQGQLWIPRR-------PNALDVSVGGAVQSGETYEEAFRREAREELNVEIDALSWRPLASFSPFQTTLSSFMCVYELRSDATPIFNPNDISGGEWLTPEHLLARIAAGEAAKGDLAELVRRCYR 168
                                    16        26        36        46      |  -    |   66        76        86        96       106       116       126       136       146       156       166  
                                                                         53      61

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with Y079_DEIRA | Q9RY71 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:162
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166  
           Y079_DEIRA     7 ERLDLVNERDEVVGQILRTDPALRWERVRVVNAFLRNSQGQLWIPRRSPSKSLFPNALDVSVGGAVQSGETYEEAFRREAREELNVEIDALSWRPLASFSPFQTTLSSFMCVYELRSDATPIFNPNDISGGEWLTPEHLLARIAAGEAAKGDLAELVRRCYR 168
               SCOP domains d2o5fb_ B: Hypothetical protein DR0079                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------NUDIX-2o5fB01 B:33-167                                                                                                                 - Pfam domains (1)
           Pfam domains (2) --------------------------NUDIX-2o5fB02 B:33-167                                                                                                                 - Pfam domains (2)
         Sec.struct. author .eeeee.....eeeeee......hhhh.eeeeeeee.....eeeeee..............eeee.....hhhhhhhhhhhhhhh.hhhhheeeeeeee.........eeeeeeee...........eeeeeeehhhhhhhhhhhh.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------NUDIX  PDB: B:32-162 UniProt: 32-162                                                                                               ------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------NUDIX_BOX  PDB: B:70-9----------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o5f B   7 ERLDLVNERDEVVGQILRTDPALRWERVRVVNAFLRNSQGQLWIPRRSPSKSLFPNALDVSVGGAVQSGETYEEAFRREAREELNVEIDALSWRPLASFSPFQTTLSSFMCVYELRSDATPIFNPNDISGGEWLTPEHLLARIAAGEAAKGDLAELVRRCYR 168
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Nudix (141)

Superfamily: Nudix (141)

Family: IPP isomerase-like (23)

Protein domain: Hypothetical protein DR0079 (2)

Deinococcus radiodurans str. R1 (Deinococcus radiodurans R1) [TaxId: 243230] (1)

1a	d2o5fa_	A:
1b	d2o5fb_	B:

(no "CATH Domain" information available for 2O5F)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Deinococcus radiodurans (8)

1a	NUDIX-2o5fB01	B:33-167
1b	NUDIX-2o5fB02	B:33-167

Asymmetric Unit(hide GO term definitions)

Chain A,B (Y079_DEIRA | Q9RY71)


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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.

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	Y079_DEIRA \| Q9RY71	:	1q27

1q27	SOLUTION NMR STRUCTURE OF DR0079

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