1VIU - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (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,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (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, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YFFH, B2467
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1VIU)

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDK_ECOLI	43-180	4	A:43-180 B:43-180 C:43-180 D:43-180

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDK_ECOLI	43-180	2	A:43-180 B:43-180 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDK_ECOLI	43-180	2	- - C:43-180 D:43-180

(no "Exon" information available for 1VIU)

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:180
 aligned with NUDK_ECOLI | P37128 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:189
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
           NUDK_ECOLI     3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
               SCOP domains d1viua_ A: ADP-ribose pyrophosphatase homologue YffH                                                                                                                                          SCOP domains
               CATH domains 1viuA00 A:3-191 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeee.......eeeeeeeee...eeeeeeee....eeeeeeeehhhhhh......eeee.eeee....hhhhhhhhhhhhhhh......eeeeeee........eeeeeeee......---------..eeeeeeehhhhhhhhhh....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------NUDIX  PDB: A:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viu A   3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYmSPGGVTELIHFFIAEYSDNQR---------EDIEVLELPFSQALEmIKTGEIRDGKTVLLLNYLQTSHLmD 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132        |-       152       162   |   172       182       | 
                                                                                                                                               120-MSE              141       151            166-MSE                 190-MSE

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with NUDK_ECOLI | P37128 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:189
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
           NUDK_ECOLI     3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
               SCOP domains d1viub_ B: ADP-ribose pyrophosphatase homologue YffH                                                                                                                                          SCOP domains
               CATH domains 1viuB00 B:3-191 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeee....eeeeeeeehhhhhh......eeee.eeee....hhhhhhhhhhhhhhh......eeeeeee........eeeeeeee.......--------..eeeeeeehhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------NUDIX  PDB: B:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viu B   3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYmSPGGVTELIHFFIAEYSDNQRA--------EDIEVLELPFSQALEmIKTGEIRDGKTVLLLNYLQTSHLmD 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162   |   172       182       | 
                                                                                                                                               120-MSE               142      151            166-MSE                 190-MSE

Chain C from PDB  Type:PROTEIN  Length:175
 aligned with NUDK_ECOLI | P37128 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       
           NUDK_ECOLI     4 QITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLM 190
               SCOP domains d1viuc_ C: ADP-ribose pyr   ophosphatase homologue YffH                                                                                                                                     SCOP domains
               CATH domains 1viuC00 C:4-189 Nucleosid   e Triphosphate Pyrophosphohydrolase                                                                                                                           - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....eeeeeeeee.---...eeeeeeeee...eeeeeeee....eeeeeeeehhhhhh......eeee.eeee....hhhhhhhhhhhhhhh......eeeeeee........eeeeeeee.hhhhh---------...eeeeeehhhhhhhhhh....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------NUDIX  PDB: C:43-180 UniProt: 43-180                                                                                                      ---------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viu C   4 QITLIKDKILSDNYFTLHNITYDLT---GEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYmSPGGVTELIHFFIAEYSDNQR---------EDIEVLELPFSQALEmIKTGEIRDGKTVLLLNYLQTSHLm 190
                                    13        23    |   33        43        53        63        73        83        93       103       113      |123       133       | -       153       163  |    173       183      |
                                                   28  32                                                                                     120-MSE              141       151            166-MSE                 190-MSE

Chain D from PDB  Type:PROTEIN  Length:179
 aligned with NUDK_ECOLI | P37128 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:188
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182        
           NUDK_ECOLI     3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLM 190
               SCOP domains d1viud_ D: ADP-ribose pyrophosphatase homologue YffH                                                                                                                                         SCOP domains
               CATH domains 1viuD00 D:3-189 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                               - CATH domains
           Pfam domains (1) -----------------------------------------NUDIX-1viuD01 D:44-184                                                                                                                       ------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------NUDIX-1viuD02 D:44-184                                                                                                                       ------ Pfam domains (2)
           Pfam domains (3) -----------------------------------------NUDIX-1viuD03 D:44-184                                                                                                                       ------ Pfam domains (3)
           Pfam domains (4) -----------------------------------------NUDIX-1viuD04 D:44-184                                                                                                                       ------ Pfam domains (4)
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeee....eeeeeeeehhhhhh......eeee.eeee....hhhhhhhhhhhhhhh......eeeeeee........eeeeeeee.......---------.eeeeeeehhhhhhhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------NUDIX  PDB: D:43-180 UniProt: 43-180                                                                                                      ---------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viu D   3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYmSPGGVTELIHFFIAEYSDNQRA---------DIEVLELPFSQALEmIKTGEIRDGKTVLLLNYLQTSHLm 190
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162   |   172       182       |
                                                                                                                                               120-MSE               142       152           166-MSE                 190-MSE

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 homologue YffH (5)

Escherichia coli [TaxId: 562] (5)

1a	d1viua_	A:
1b	d1viub_	B:
1c	d1viuc_	C:
1d	d1viud_	D:

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	1viuC00	C:4-189
1b	1viuD00	D:3-189
1c	1viuA00	A:3-191
1d	1viuB00	B:3-191

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Escherichia coli (strain K12) (28)

1a	NUDIX-1viuD01	D:44-184
1b	NUDIX-1viuD02	D:44-184
1c	NUDIX-1viuD03	D:44-184
1d	NUDIX-1viuD04	D:44-184

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NUDK_ECOLI | P37128)


GO:0052751	GDP-mannose hydrolase activity	Catalysis of the reaction: GDP-mannose + H2O = GMP + mannose-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.

Asymmetric Unit
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Description

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