1G9Q - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   COMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP-RIBOSE

Authors :   S. B. Gabelli, M. A. Bianchet, M. J. Bessman, L. M. Amzel

Date :   27 Nov 00 (Deposition) - 02 May 01 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

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

Reference :   S. B. Gabelli, M. A. Bianchet, M. J. Bessman, L. M. Amzel
The Structure Of Adp-Ribose Pyrophosphatase Reveals The Structural Basis For The Versatility Of The Nudix Family.
Nat. Struct. Biol. V. 8 467 2001
PubMed-ID: 11323725 | Reference-DOI: 10.1038/87647

Molecule 1 - HYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGION
	Chains	:	A, B
	EC Number	:	3.6.1.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ORF209
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ADP-RIBOSE PYROPHOSPHATASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	APR	2	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:17 , ILE A:18 , ILE A:19 , PHE A:28 , PHE A:29 , ARG A:37 , ARG A:56 , ARG A:79 , MET A:98 , GLU A:139 , SER A:141 , HOH A:217 , HOH A:246 , HOH A:252 , ARG B:50 , ARG B:51 , GLU B:52 , SER B:133 , GLY B:135 , HOH B:332 , HOH B:385	BINDING SITE FOR RESIDUE APR B 301
2	AC2	SOFTWARE	ARG A:51 , GLU A:52 , SER A:133 , GLY A:135 , PHE B:28 , PHE B:29 , ARG B:56 , ARG B:79 , ALA B:96 , GLY B:97 , MET B:98 , GLU B:112 , GLU B:139 , ASN B:163 , HOH B:303 , HOH B:327 , HOH B:353 , HOH B:407	BINDING SITE FOR RESIDUE APR B 302

(no "SS Bond" information available for 1G9Q)

(no "Cis Peptide Bond" information available for 1G9Q)

(no "SAP(SNP)/Variant" information available for 1G9Q)

Asymmetric/Biological Unit (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:55-193 B:55-193
2	NUDIX_BOX	PS00893	Nudix box signature.	ADPP_ECOLI	97-118	2	A:97-118 B:97-118

(no "Exon" information available for 1G9Q)

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:205
 aligned with ADPP_ECOLI | Q93K97 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           ADPP_ECOLI     1 MLKPDNLPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
               SCOP domains d1g9qa_ A: ADP-ribose pyrophosphatase                                                                                                                                                                             SCOP domains
               CATH domains 1g9qA00 A:1-209 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeeeeeee....eeeeeeeee..........eeeeeee...eeeeeeee....eeeeeeee.hhhhhhh...eeee.eeee.....hhhhhhhhhhhhhhh.....eeeeeeee........eeeeeeee.hhhhh.----........eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------NUDIX  PDB: A:55-193 UniProt: 55-193                                                                                                       ---------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g9q A   1 MLKPDNLPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTAS----LADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   |   160       170       180       190       200         
                                                                                                                                                                                   154  159

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with ADPP_ECOLI | Q93K97 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:202
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207  
           ADPP_ECOLI     8 PVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
               SCOP domains d1g9qb_ B: ADP-ribose pyrophosphatase                                                                                                                                                                      SCOP domains
               CATH domains 1g9qB00 B:8-209 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:55-193 UniProt: 55-193                                                                                                       ---------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g9q B   8 PVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207

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: 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	d1g9qa_	A:
1b	d1g9qb_	B:

Asymmetric/Biological 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	1g9qB00	B:8-209
1b	1g9qA00	A:1-209

(no "Pfam Domain" information available for 1G9Q)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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/Biological Unit
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	Cis Peptide Bonds
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	1g9q
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	3.6.1.13
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	ADPP_ECOLI \| Q93K97	:	1g0s 1ga7 1khz 1viq

1g0s	1G0S IS THE STRUCTURE OF ADP-RIBOSE PYROPHOSPHATASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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