1FEZ - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF BACILLUS CEREUS PHOSPHONOACETALDEHYDE HYDROLASE COMPLEXED WITH TUNGSTATE, A PRODUCT ANALOG

Authors :   M. C. Morais, W. Zhang, A. S. Baker, G. Zhang, D. Dunaway-Mariano, K. N. Allen

Date :   24 Jul 00 (Deposition) - 04 Oct 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Had-Family Alpha/Beta Core Domain, Mg(Ii) Binding Site, 5- Helix Bundle, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Morais, W. Zhang, A. S. Baker, G. Zhang, D. Dunaway-Mariano, K. N. Allen
The Crystal Structure Of Bacillus Cereus Phosphonoacetaldehyde Hydrolase: Insight Into Catalysis Of Phosphorus Bond Cleavage And Catalytic Diversification Within The Had Enzyme Superfamily.
Biochemistry V. 39 10385 2000
PubMed-ID: 10956028 | Reference-DOI: 10.1021/BI001171J
(for further references see the PDB file header)

Molecule 1 - PHOSPHONOACETALDEHYDE HYDROLASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK223-3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS CEREUS
	Organism Taxid	:	1396

		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 (2, 6)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	WO4	2	Ligand/Ion	TUNGSTATE(VI)ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	WO4	1	Ligand/Ion	TUNGSTATE(VI)ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	WO4	1	Ligand/Ion	TUNGSTATE(VI)ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:12 , TRP B:13 , ALA B:14 , THR B:126 , GLY B:127 , TYR B:128 , ARG B:160 , HOH B:405 , HOH B:407 , MG B:802	BINDING SITE FOR RESIDUE WO4 B 800
2	AC2	SOFTWARE	ASP A:12 , ALA A:14 , ASP A:186	BINDING SITE FOR RESIDUE MG A 801
3	AC3	SOFTWARE	ASP B:12 , ALA B:14 , GLY B:15 , ASP B:186 , THR B:187 , SER B:209 , HOH B:405 , WO4 B:800	BINDING SITE FOR RESIDUE MG B 802
4	AC4	SOFTWARE	ASP D:12 , TRP D:13 , ALA D:14 , GLY D:50 , THR D:126 , GLY D:127 , TYR D:128 , ARG D:160 , HOH D:413 , HOH D:415 , MG D:805	BINDING SITE FOR RESIDUE WO4 D 803
5	AC5	SOFTWARE	ASP C:12 , ALA C:14 , ASP C:186	BINDING SITE FOR RESIDUE MG C 804
6	AC6	SOFTWARE	ASP D:12 , ALA D:14 , GLY D:15 , ASP D:186 , THR D:187 , SER D:209 , HOH D:413 , WO4 D:803	BINDING SITE FOR RESIDUE MG D 805

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

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

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

(no "PROSITE Motif" information available for 1FEZ)

(no "Exon" information available for 1FEZ)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:256
 aligned with PHNX_BACCE | O31156 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           PHNX_BACCE     2 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 257
               SCOP domains d1feza_ A: Phosphonoacetaldehyde hydrolase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1fezA01            1fezA02 A:24-101 Putative phosphatase; domain 2                               1fezA01 A:5-23,A:102-260  [code=3.40.50.1000, no name defined]                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhhhhh.....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...................hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh..eeee.................hhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fez A   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 260
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with PHNX_BACCE | O31156 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           PHNX_BACCE     2 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 257
               SCOP domains d1fezb_ B: Phosphonoacetaldehyde hydrolase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1fezB01            1fezB02 B:24-101 Putative phosphatase; domain 2                               1fezB01 B:5-23,B:102-260  [code=3.40.50.1000, no name defined]                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhhhh.......hhhhh....hhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...................hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.................hhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fez B   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 260
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

Chain C from PDB  Type:PROTEIN  Length:256
 aligned with PHNX_BACCE | O31156 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           PHNX_BACCE     2 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 257
               SCOP domains d1fezc_ C: Phosphonoacetaldehyde hydrolase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1fezC01            1fezC02 C:24-101 Putative phosphatase; domain 2                               1fezC01 C:5-23,C:102-260  [code=3.40.50.1000, no name defined]                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhhhhh.....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...................hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh..eeee.................hhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fez C   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 260
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

Chain D from PDB  Type:PROTEIN  Length:256
 aligned with PHNX_BACCE | O31156 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           PHNX_BACCE     2 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 257
               SCOP domains d1fezd_ D: Phosphonoacetaldehyde hydrolase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1fezD01            1fezD02 D:24-101 Putative phosphatase; domain 2                               1fezD01 D:5-23,D:102-260  [code=3.40.50.1000, no name defined]                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhhhh.......hhhhh....hhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...................hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.................hhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fez D   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 260
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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: Phosphonoacetaldehyde hydrolase-like (9)

Protein domain: Phosphonoacetaldehyde hydrolase (6)

Bacillus cereus [TaxId: 1396] (6)

1a	d1feza_	A:
1b	d1fezb_	B:
1c	d1fezc_	C:
1d	d1fezd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1000, no name defined] (211)

Bacillus cereus. Organism_taxid: 1396. (8)

1a	1fezA01	A:5-23,A:102-260
1b	1fezB01	B:5-23,B:102-260
1c	1fezC01	C:5-23,C:102-260
1d	1fezD01	D:5-23,D:102-260

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: Putative phosphatase; domain 2 (65)

Bacillus cereus. Organism_taxid: 1396. (8)

2a	1fezA02	A:24-101
2b	1fezB02	B:24-101
2c	1fezC02	C:24-101
2d	1fezD02	D:24-101

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PHNX_BACCE | O31156)

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: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.
	GO:0050194	phosphonoacetaldehyde hydrolase activity	Catalysis of the reaction: H(2)O + phosphonoacetaldehyde = acetaldehyde + H(+) + phosphate.
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.
	GO:0019700	organic phosphonate catabolic process	The chemical reactions and pathways resulting in the breakdown of phosphonates, any organic compound containing one or more C-PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Catabolism of phosphonic acid itself, an inorganic compound without the biochemically relevant C-P bond, is not included.

Asymmetric Unit
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	1fez
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Description

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