1VIQ - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PUTATIVE ADP RIBOSE PYROPHOSPHATASE

Authors :   Structural Genomix

Date :   01 Dec 03 (Deposition) - 30 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (2x)
Biol. Unit 2: B,C  (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: B  (1x)
Biol. Unit 5: C  (1x)

Keywords :   Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622 | Reference-DOI: 10.1002/PROT.20541

Molecule 1 - ADP-RIBOSE PYROPHOSPHATASE
	Chains	:	A, B, C
	EC Number	:	3.6.1.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NUDF, B3034, C3780, Z4391, ECS3922, SF3074, S3279
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ADP-RIBOSE DIPHOSPHATASE, ADENOSINE DIPHOSPHORIBOSE PYROPHOSPHATASE, ADPR-PPASE, ADP-RIBOSE PHOSPHOHYDROLASE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:		B	C
Biological Unit 3 (1x)	:	A
Biological Unit 4 (1x)	:		B
Biological Unit 5 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1VIQ)

(no "Site" information available for 1VIQ)

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

Asymmetric Unit

No.	Residues
1	Leu A:6	-	Pro A:7

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

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	ADPP_ECOLI	55-193	3	A:54-192 B:54-192 C:54-192
2	NUDIX_BOX	PS00893	Nudix box signature.	ADPP_ECOLI	97-118	3	A:96-117 B:96-117 C:96-117

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	ADPP_ECOLI	55-193	2	A:54-192 - -
2	NUDIX_BOX	PS00893	Nudix box signature.	ADPP_ECOLI	97-118	2	A:96-117 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	ADPP_ECOLI	55-193	2	- B:54-192 C:54-192
2	NUDIX_BOX	PS00893	Nudix box signature.	ADPP_ECOLI	97-118	2	- B:96-117 C:96-117

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	ADPP_ECOLI	55-193	1	A:54-192 - -
2	NUDIX_BOX	PS00893	Nudix box signature.	ADPP_ECOLI	97-118	1	A:96-117 - -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	ADPP_ECOLI	55-193	1	- B:54-192 -
2	NUDIX_BOX	PS00893	Nudix box signature.	ADPP_ECOLI	97-118	1	- B:96-117 -

Biological Unit 5 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	ADPP_ECOLI	55-193	1	- - C:54-192
2	NUDIX_BOX	PS00893	Nudix box signature.	ADPP_ECOLI	97-118	1	- - C:96-117

(no "Exon" information available for 1VIQ)

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:204
 aligned with ADPP_ECOLI | Q93K97 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           ADPP_ECOLI     1 MLKPDNLPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEW 208
               SCOP domains d1viqa_ A: ADP-ribose pyrophosphatase                                                                                                                                                                            SCOP domains
               CATH domains 1viqA00 A:0-207 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeeeeeeee...eeeeeeeee..........eeeeeee...eeeeeeee....eeeeeeee.hhhhhhh...eeee.eeee.....hhhhhhhhhhhhh.......eeeeeeee........eeeeeeee.hhhhh..ee.----...eeeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------NUDIX  PDB: A:54-192 UniProt: 55-193                                                                                                       --------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viq A   0 SLKPDNLPVTFGKNDVEIIARETLYRGFSSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHG----NEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEW 207
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       | -  |    169       179       189       199        
                                                                                                                                                                                       157  162

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with ADPP_ECOLI | Q93K97 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           ADPP_ECOLI     1 MLKPDNLPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEW 208
               SCOP domains d1viqb_ B: ADP-ribose pyrophosphatase                                                                                                                                                                            SCOP domains
               CATH domains 1viqB00 B:0-207 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeeeeeeee...eeeeeeeee..........eeeeeee..eeeeeeeee....eeeeeeee.hhhhhhh...eeee.eeeee....hhhhhhhhhhhhhhh.....eeeeeeee........eeeeeeee.hhhhh....-------..eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------NUDIX  PDB: B:54-192 UniProt: 55-193                                                                                                       --------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viq B   0 SLKPDNLPVTFGKNDVEIIARETLYRGFSSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIH-------DIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEW 207
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149      |  -    |  169       179       189       199        
                                                                                                                                                                                      156     164

Chain C from PDB  Type:PROTEIN  Length:194
 aligned with ADPP_ECOLI | Q93K97 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:203
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
           ADPP_ECOLI     7 LPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
               SCOP domains d1viqc_ C: ADP-ribose pyrophosphatase                                                                                                                                                                       SCOP domains
               CATH domains 1viqC00 C:6-208 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                                CATH domains
           Pfam domains (1) -------------------------------------------------NUDIX-1viqC01 C:55-197                                                                                                                         ----------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------NUDIX-1viqC02 C:55-197                                                                                                                         ----------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------NUDIX-1viqC03 C:55-197                                                                                                                         ----------- Pfam domains (3)
         Sec.struct. author .....hhh.eeeeee...ee...eeeeeeeee..........eeeeeee...eeeeeeee....eeeeeeee.hhhhhhh...eeee.eeee.....hhhhhhhhhhhhhhh.....eeeeeeee........eeeeeeee.hhhhh---------....eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------NUDIX  PDB: C:54-192 UniProt: 55-193                                                                                                       ---------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viq C   6 LPVTFGKNDVEIIARETLYRGFSSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTA---------NEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 208
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145      |  -      |165       175       185       195       205   
                                                                                                                                                                            152       162

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Nudix (141)

Superfamily: Nudix (141)

Family: MutT-like (82)

Protein domain: ADP-ribose pyrophosphatase (21)

Escherichia coli [TaxId: 562] (5)

1a	d1viqa_	A:
1b	d1viqc_	C:
1c	d1viqb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Nucleoside Triphosphate Pyrophosphohydrolase (89)

Homologous Superfamily: Nucleoside Triphosphate Pyrophosphohydrolase (89)

Escherichia coli. Organism_taxid: 562. (17)

1a	1viqC00	C:6-208
1b	1viqB00	B:0-207
1c	1viqA00	A:0-207

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Escherichia coli (strain K12) (28)

1a	NUDIX-1viqC01	C:55-197
1b	NUDIX-1viqC02	C:55-197
1c	NUDIX-1viqC03	C:55-197

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (ADPP_ECOLI | Q93K97)

molecular function
	GO:0047631	ADP-ribose diphosphatase activity	Catalysis of the reaction: ADP-ribose + H2O = AMP + D-ribose 5-phosphate.
	GO:0019144	ADP-sugar diphosphatase activity	Catalysis of the reaction: ADP-sugar + H2O = AMP + sugar 1-phosphate.
	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:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
	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.
biological process
	GO:0009408	response to heat	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
cellular component
	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 Unit
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	Cis Peptide Bonds
		Leu A:6 - Pro A:7	[ RasMol ]

Biological Units
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	1viq
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	3.6.1.13
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	ADPP_ECOLI \| Q93K97	:	1g0s 1g9q 1ga7 1khz

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