3QYP - JenaLib

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Title :   CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, GLU47ASN MUTANT COMPLEXED WITH CALCIUM AND PHOSPHATE

Authors :   Y. Patskovsky, H. Huang, R. Toro, J. A. Gerlt, S. K. Burley, D. Dunaway-M S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc), Enzyme Function Initiative(Efi)

Date :   03 Mar 11 (Deposition) - 13 Apr 11 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Hydrolase, Pyrophosphatase, Magnesium Binding Site, New York Sgx Research Center For Structural Genomics, Nysgx Enzyme Function Initiative, Efi, Psi-2, Protein Structure Initiative, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Huang, Y. Patskovsky, R. Toro, J. D. Farelli, C. Pandya, S. C. Almo, K. N. Allen, D. Dunaway-Mariano
Divergence Of Structure And Function In The Haloacid Dehalogenase Enzyme Superfamily: Bacteroides Thetaiotaomicron Bt2127 Is An Inorganic Pyrophosphatase.
Biochemistry V. 50 8937 2011
PubMed-ID: 21894910 | Reference-DOI: 10.1021/BI201181Q

Molecule 1 - INORGANIC PYROPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BT_2127
	Mutation	:	YES
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON
	Organism Taxid	:	818
	Synonym	:	PUTATIVE BETA-PHOSPHOGLUCOMUTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 8)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	PO4	2	Ligand/Ion	PHOSPHATE ION
5	UNL	1	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	-1	Ligand/Ion	GLYCEROL
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	UNL	-1	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	UNL	1	Ligand/Ion	UNKNOWN LIGAND

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:11 , MET A:12 , ASP A:13 , ASN A:47 , GLY A:48 , THR A:113 , GLY A:114 , SER A:115 , LYS A:147 , CA A:226 , HOH A:330 , HOH A:423 , HOH A:424 , HOH A:425	BINDING SITE FOR RESIDUE PO4 A 225
2	AC2	SOFTWARE	ASP A:11 , ASP A:13 , ASN A:47 , ASN A:172 , PO4 A:225 , HOH A:293 , HOH A:425	BINDING SITE FOR RESIDUE CA A 226
3	AC3	SOFTWARE	LYS A:79 , GLN A:117	BINDING SITE FOR RESIDUE CL A 227
4	AC4	SOFTWARE	GLU B:166 , HOH B:255 , HOH B:429 , HOH B:471 , HOH B:475	BINDING SITE FOR RESIDUE CA B 225
5	AC5	SOFTWARE	ASP B:11 , MET B:12 , ASP B:13 , ASN B:47 , GLY B:48 , THR B:113 , GLY B:114 , SER B:115 , LYS B:147 , CA B:227 , GOL B:228 , HOH B:420 , HOH B:421 , HOH B:422 , HOH B:426	BINDING SITE FOR RESIDUE PO4 B 226
6	AC6	SOFTWARE	ASP B:11 , ASP B:13 , ASN B:47 , ASN B:172 , PO4 B:226 , HOH B:362 , HOH B:422	BINDING SITE FOR RESIDUE CA B 227
7	AC7	SOFTWARE	ASP B:13 , MET B:20 , TRP B:27 , ALA B:43 , ASN B:47 , PO4 B:226 , HOH B:426 , HOH B:432 , HOH B:433	BINDING SITE FOR RESIDUE GOL B 228

(no "SS Bond" information available for 3QYP)

Asymmetric Unit

No.	Residues
1	Lys A:147	-	Pro A:148
2	Lys B:147	-	Pro B:148

(no "SAP(SNP)/Variant" information available for 3QYP)

(no "PROSITE Motif" information available for 3QYP)

(no "Exon" information available for 3QYP)

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:221
 aligned with Q8A5V9_BACTN | Q8A5V9 from UniProtKB/TrEMBL  Length:224

    Alignment length:221
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
         Q8A5V9_BACTN     4 KLKAVLFDMDGVLFNSMPYHSEAWHQVMKTHGLDLSREEAYMHEGRTGASTINIVFQRELGKEATQEEIESIYHEKSILFNSYPEAERMPGAWELLQKVKSEGLTPMVVTGSGQLSLLERLEHNFPGMFHKELMVTAFDVKYGKPNPEPYLMALKKGGLKADEAVVIENAPLGVEAGHKAGIFTIAVNTGPLDGQVLLDAGADLLFPSMQTLCDSWDTIML 224
               SCOP domains d3qypa_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh....hhh.ee...........hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.....hhhhhhhh...eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyp A   4 KLKAVLFDMDGVLFNSMPYHSEAWHQVMKTHGLDLSREEAYMHNGRTGASTINIVFQRELGKEATQEEIESIYHEKSILFNSYPEAERMPGAWELLQKVKSEGLTPMVVTGSGQLSLLERLEHNFPGMFHKELMVTAFDVKYGKPNPEPYLMALKKGGLKADEAVVIENAPLGVEAGHKAGIFTIAVNTGPLDGQVLLDAGADLLFPSMQTLCDSWDTIML 224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with Q8A5V9_BACTN | Q8A5V9 from UniProtKB/TrEMBL  Length:224

    Alignment length:228
                                1                                                                                                                                                                                                                               
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        
         Q8A5V9_BACTN     - ----MRKKLKAVLFDMDGVLFNSMPYHSEAWHQVMKTHGLDLSREEAYMHEGRTGASTINIVFQRELGKEATQEEIESIYHEKSILFNSYPEAERMPGAWELLQKVKSEGLTPMVVTGSGQLSLLERLEHNFPGMFHKELMVTAFDVKYGKPNPEPYLMALKKGGLKADEAVVIENAPLGVEAGHKAGIFTIAVNTGPLDGQVLLDAGADLLFPSMQTLCDSWDTIML 224
               SCOP domains d3qypb_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------HAD_2-3qypB01 B:8-190                                                                                                                                                                  ---------------------------------- Pfam domains (1)
           Pfam domains (2) -----------HAD_2-3qypB02 B:8-190                                                                                                                                                                  ---------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhh.eeee......eehhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....ee..hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh....hhh.eehhhhh......hhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh..eeeee.....hhhhhhhh...eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qyp B  -3 RGSHMRKKLKAVLFDMDGVLFNSMPYHSEAWHQVMKTHGLDLSREEAYMHNGRTGASTINIVFQRELGKEATQEEIESIYHEKSILFNSYPEAERMPGAWELLQKVKSEGLTPMVVTGSGQLSLLERLEHNFPGMFHKELMVTAFDVKYGKPNPEPYLMALKKGGLKADEAVVIENAPLGVEAGHKAGIFTIAVNTGPLDGQVLLDAGADLLFPSMQTLCDSWDTIML 224
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216

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) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: automated matches (99)

Protein domain: automated matches (99)

Bacteroides thetaiotaomicron [TaxId: 818] (21)

1a	d3qypa_	A:
1b	d3qypb_	B:

(no "CATH Domain" information available for 3QYP)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: HAD_2 (33)

Bacteroides thetaiotaomicron (14)

1a	HAD_2-3qypB01	B:8-190
1b	HAD_2-3qypB02	B:8-190

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8A5V9_BACTN | Q8A5V9)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:147 - Pro A:148	[ RasMol ]
		Lys B:147 - Pro B:148	[ RasMol ]

Biological Units
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3qu2	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, A CLOSED CAP CONFORMATION, WILD-TYPE PROTEIN
3qu4	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP13ALA MUTANT
3qu5	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP11ASN MUTANT
3qu7	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP13ASN MUTANT COMPLEXED WITH CALCIUM AND PHOSPHATE
3qu9	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP13ASN MUTANT COMPLEXED WITH MAGNESIUM AND TARTRATE
3qub	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, GLU47ALA MUTANT COMPLEXED WITH SULFATE
3quc	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, GLU47ASN MUTANT COMPLEXED WITH SULFATE
3quq	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, AN OPEN CAP CONFORMATION, WILD-TYPE PROTEIN
3qut	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP13ASN MUTANT, AN OPEN CAP CONFORMATION
3qx7	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON COMPLEXED WITH PHOSPHATE, A CLOSED CAP CONFORMATION, WILD-TYPE PROTEIN
3qxg	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON COMPLEXED WITH CALCIUM, A CLOSED CAP CONFORMATION, WILD-TYPE PROTEIN
3r9k	CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, GLU47ASP MUTANT COMPLEXED WITH SULFATE, A CLOSED CAP CONFORMATION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 8)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (3, 3)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File