1YGZ - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM HELICOBACTER PYLORI

Authors :   C. A. Wu, N. K. Lokanath, D. Y. Kim, H. J. Park, H. Y. Hwang, S. T. Kim, S. W. S K. K. Kim

Date :   06 Jan 05 (Deposition) - 01 Nov 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

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

Reference :   C. A. Wu, N. K. Lokanath, D. Y. Kim, H. J. Park, H. Y. Hwang, S. T. Kim, S. W. Suh, K. K. Kim
Structure Of Inorganic Pyrophosphatase From Helicobacter Pylori.
Acta Crystallogr. , Sect. D V. 61 1459 2005
PubMed-ID: 16239722 | Reference-DOI: 10.1107/S0907444905025667

Molecule 1 - INORGANIC PYROPHOSPHATASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	3.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	85962
	Strain	:	26695
	Synonym	:	PYROPHOSPHATE PHOSPHO- HYDROLASE, PPASE

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C	D	E	F
Biological Unit 2 (3x)	:					E	F
Biological Unit 3 (3x)	:	A	B
Biological Unit 4 (3x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 24)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 24)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 24)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 24)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 24)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1YGZ)

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

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

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PPASE	PS00387	Inorganic pyrophosphatase signature.	IPYR_HELPY	64-70	6	A:64-70 B:64-70 C:64-70 D:64-70 E:64-70 F:64-70

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PPASE	PS00387	Inorganic pyrophosphatase signature.	IPYR_HELPY	64-70	6	A:64-70 B:64-70 C:64-70 D:64-70 E:64-70 F:64-70

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PPASE	PS00387	Inorganic pyrophosphatase signature.	IPYR_HELPY	64-70	6	- - - - E:64-70 F:64-70

Biological Unit 3 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PPASE	PS00387	Inorganic pyrophosphatase signature.	IPYR_HELPY	64-70	6	A:64-70 B:64-70 - - - -

Biological Unit 4 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PPASE	PS00387	Inorganic pyrophosphatase signature.	IPYR_HELPY	64-70	6	- - C:64-70 D:64-70 - -

(no "Exon" information available for 1YGZ)

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:172
 aligned with IPYR_HELPY | P56153 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           IPYR_HELPY     1 MNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALMVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNMEDESGMDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
               SCOP domains d1ygza_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains -1ygzA00 A:2-172 Inorganic Pyrophosphatase                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...ee..eeeeeeee.....eeeeee....eeeeeee.........eeee............eeee..........eeeeeeeeeeeeee......eeeeee....hhhhh...hhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------PPASE  ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ygz A   1 mNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALmVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNmEDESGmDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
                            |       10        20        30        40        50        60        70        80        90   |   100       110       120       130       140       150       160       170  
                            |                                    39-MSE                                                 94-MSE |                                                                        
                            1-MSE                                                                                            100-MSE

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with IPYR_HELPY | P56153 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           IPYR_HELPY     1 MNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALMVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNMEDESGMDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
               SCOP domains d1ygzb_ B: automated matches                                                                                                                                                 SCOP domains
               CATH domains -1ygzB00 B:2-172 Inorganic Pyrophosphatase                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...ee..eeeeeeee.....eeeee......eeeeee.........eeee............eeee..........eeeeeeeeeeeeee......eeeeee....hhhhh...hhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------PPASE  ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ygz B   1 mNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALmVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNmEDESGmDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
                            |       10        20        30        40        50        60        70        80        90   |   100       110       120       130       140       150       160       170  
                            1-MSE                                39-MSE                                                 94-MSE |                                                                        
                                                                                                                             100-MSE

Chain C from PDB  Type:PROTEIN  Length:172
 aligned with IPYR_HELPY | P56153 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           IPYR_HELPY     1 MNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALMVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNMEDESGMDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
               SCOP domains d1ygzc_ C: automated matches                                                                                                                                                 SCOP domains
               CATH domains -1ygzC00 C:2-172 Inorganic Pyrophosphatase                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...ee..eeeeeeee.....eeeeee....eeeeeee.........eeee............eeee..........eeeeeeeeeeeeee......eeeeee....hhhhh...hhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------PPASE  ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ygz C   1 mNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALmVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNmEDESGmDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
                            |       10        20        30        40        50        60        70        80        90   |   100       110       120       130       140       150       160       170  
                            1-MSE                                39-MSE                                                 94-MSE |                                                                        
                                                                                                                             100-MSE

Chain D from PDB  Type:PROTEIN  Length:172
 aligned with IPYR_HELPY | P56153 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           IPYR_HELPY     1 MNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALMVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNMEDESGMDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
               SCOP domains d1ygzd_ D: automated matches                                                                                                                                                 SCOP domains
               CATH domains -1ygzD00 D:2-172 Inorganic Pyrophosphatase                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...ee..eeeeeeee.....eeeeee....eeeeeee.........eeee............eeee..........eeeeeeeeeeeeee......eeeeee....hhhhh...hhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------PPASE  ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ygz D   1 mNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALmVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNmEDESGmDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
                            |       10        20        30        40        50        60        70        80        90   |   100       110       120       130       140       150       160       170  
                            1-MSE                                39-MSE                                                 94-MSE |                                                                        
                                                                                                                             100-MSE

Chain E from PDB  Type:PROTEIN  Length:172
 aligned with IPYR_HELPY | P56153 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           IPYR_HELPY     1 MNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALMVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNMEDESGMDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
               SCOP domains d1ygze_ E: automated matches                                                                                                                                                 SCOP domains
               CATH domains -1ygzE00 E:2-172 Inorganic Pyrophosphatase                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...ee..eeeeeeee.....eeeee......eeeeee.........eeee............eeee..........eeeeeeeeeeeeee......eeeeee....hhhhh...hhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------PPASE  ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ygz E   1 mNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALmVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNmEDESGmDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
                            |       10        20        30        40        50        60        70        80        90   |   100       110       120       130       140       150       160       170  
                            1-MSE                                39-MSE                                                 94-MSE |                                                                        
                                                                                                                             100-MSE

Chain F from PDB  Type:PROTEIN  Length:172
 aligned with IPYR_HELPY | P56153 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           IPYR_HELPY     1 MNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALMVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNMEDESGMDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
               SCOP domains d1ygzf_ F: automated matches                                                                                                                                                 SCOP domains
               CATH domains -1ygzF00 F:2-172 Inorganic Pyrophosphatase                                                                                                                                   CATH domains
           Pfam domains (1) ---------------Pyrophosphatase-1ygzF01 F:16-172                                                                                                                              Pfam domains (1)
           Pfam domains (2) ---------------Pyrophosphatase-1ygzF02 F:16-172                                                                                                                              Pfam domains (2)
           Pfam domains (3) ---------------Pyrophosphatase-1ygzF03 F:16-172                                                                                                                              Pfam domains (3)
           Pfam domains (4) ---------------Pyrophosphatase-1ygzF04 F:16-172                                                                                                                              Pfam domains (4)
           Pfam domains (5) ---------------Pyrophosphatase-1ygzF05 F:16-172                                                                                                                              Pfam domains (5)
           Pfam domains (6) ---------------Pyrophosphatase-1ygzF06 F:16-172                                                                                                                              Pfam domains (6)
         Sec.struct. author .hhhhh...ee..eeeeeeee.....eeeeee....eeeeeee.........eeee............eeee..........eeeeeeeeeeeeee......eeeeee....hhhhh...hhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------PPASE  ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ygz F   1 mNLEKLEVSHDADSLCVVIEISKHSNIKYELDKESGALmVDRVLYGAQNYPANYGFVPNTLGSDGDPVDALVLSDVAFQAGSVVKARLVGVLNmEDESGmDEKLIALPIDKIDPTHSYVKDIDDLSKHTLDKIKHFFETYKDLEPNKWVKVKGFENKESAIKVLEKAIKAYQ 172
                            |       10        20        30        40        50        60        70        80        90   |   100       110       120       130       140       150       160       170  
                            1-MSE                                39-MSE                                                 94-MSE |                                                                        
                                                                                                                             100-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: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Inorganic pyrophosphatase (69)

Family: automated matches (13)

Protein domain: automated matches (13)

Helicobacter pylori [TaxId: 85962] (3)

1a	d1ygza_	A:
1b	d1ygzb_	B:
1c	d1ygzc_	C:
1d	d1ygzd_	D:
1e	d1ygze_	E:
1f	d1ygzf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Inorganic Pyrophosphatase (59)

Homologous Superfamily: Inorganic Pyrophosphatase (59)

Helicobacter pylori 26695. Organism_taxid: 85962. Strain: 26695. (1)

1a	1ygzA00	A:2-172
1b	1ygzB00	B:2-172
1c	1ygzC00	C:2-172
1d	1ygzD00	D:2-172
1e	1ygzE00	E:2-172
1f	1ygzF00	F:2-172

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Pyrophosphatase] (19)

Family: Pyrophosphatase (19)

Helicobacter pylori (Campylobacter pylori) (1)

1a	Pyrophosphatase-1ygzF01	F:16-172
1b	Pyrophosphatase-1ygzF02	F:16-172
1c	Pyrophosphatase-1ygzF03	F:16-172
1d	Pyrophosphatase-1ygzF04	F:16-172
1e	Pyrophosphatase-1ygzF05	F:16-172
1f	Pyrophosphatase-1ygzF06	F:16-172

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (IPYR_HELPY | P56153)

molecular function
	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:0004427	inorganic diphosphatase activity	Catalysis of the reaction: diphosphate + H(2)O = H(+) + 2 phosphate.
	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:0006796	phosphate-containing compound metabolic process	The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	IPYR_HELPY \| P56153	:	2bqx 2bqy

(no "Related Entries Specified in the PDB File" available for 1YGZ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 24)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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