2IOH - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PHOSPHONOACETALDEHYDE HYDROLASE WITH A K53R MUTATION

Authors :   K. A. Allen, S. D. Lahiri, G. Zhang, D. Dunaway-Mariano, E. Peisach

Date :   10 Oct 06 (Deposition) - 07 Aug 07 (Release) - 17 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Phosphonoacetaldehyde Hydrolase, Haloacid Dehalogenase Superfamily, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. D. Lahiri, G. Zhang, D. Dunaway-Mariano, K. N. Allen
Diversification Of Function In The Haloacid Dehalogenase Enzyme Superfamily: The Role Of The Cap Domain In Hydrolyti Phosphoruscarbon Bond Cleavage.
Bioorg. Chem. V. 34 394 2006
PubMed-ID: 17070898 | Reference-DOI: 10.1016/J.BIOORG.2006.09.007

Molecule 1 - PHOSPHONOACETALDEHYDE HYDROLASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	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 (2x)	:			C
Biological Unit 3 (2x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:12 , ALA A:14 , THR A:126 , GLY A:127 , TYR A:128 , MG A:321	BINDING SITE FOR RESIDUE PO4 A 320
2	AC2	SOFTWARE	ASP A:12 , ALA A:14 , ASP A:186 , PO4 A:320	BINDING SITE FOR RESIDUE MG A 321
3	AC3	SOFTWARE	ASP B:12 , ALA B:14 , THR B:126 , GLY B:127 , TYR B:128 , MG B:321	BINDING SITE FOR RESIDUE PO4 B 320
4	AC4	SOFTWARE	ASP B:12 , ALA B:14 , ASP B:186 , PO4 B:320	BINDING SITE FOR RESIDUE MG B 321
5	AC5	SOFTWARE	ASP C:12 , ALA C:14 , THR C:126 , GLY C:127 , TYR C:128 , MG C:321	BINDING SITE FOR RESIDUE PO4 C 320
6	AC6	SOFTWARE	ASP C:12 , ALA C:14 , ASP C:186 , PO4 C:320	BINDING SITE FOR RESIDUE MG C 321
7	AC7	SOFTWARE	ASP D:12 , ALA D:14 , THR D:126 , GLY D:127 , TYR D:128 , MG D:321	BINDING SITE FOR RESIDUE PO4 D 320
8	AC8	SOFTWARE	ASP D:12 , ALA D:14 , ASP D:186 , PO4 D:320	BINDING SITE FOR RESIDUE MG D 321

(no "SS Bond" information available for 2IOH)

(no "Cis Peptide Bond" information available for 2IOH)

(no "SAP(SNP)/Variant" information available for 2IOH)

(no "PROSITE Motif" information available for 2IOH)

(no "Exon" information available for 2IOH)

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: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 d2ioha_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2iohA01            2iohA02 A:24-101 Putative phosphatase; domain 2                               2iohA01 A:5-23,A:102-260  [code=3.40.50.1000, no name defined]                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhhhh................hhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh......eeee....hhhhhhhhhhhhhh....................hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.........hhhhhhh.hhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ioh A   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLRIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 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 d2iohb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2iohB01            2iohB02 B:24-101 Putative phosphatase; domain 2                               2iohB01 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................hhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh......eeee....hhhhhhhhhhhhhh....................hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.........hhhhhhh.hhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ioh B   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLRIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 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 d2iohc_ C: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2iohC01            2iohC02 C:24-101 Putative phosphatase; domain 2                               2iohC01 C:5-23,C:102-260  [code=3.40.50.1000, no name defined]                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhhhh................hhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh......eeee....hhhhhhhhhhhhhh....................hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.........hhhhhhh.hhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ioh C   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLRIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 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 d2iohd_ D: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2iohD01            2iohD02 D:24-101 Putative phosphatase; domain 2                               2iohD01 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................hhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh......eeee....hhhhhhhhhhhhhh....................hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.........hhhhhhh.hhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ioh D   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLRIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 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: automated matches (2)

Bacillus cereus [TaxId: 1396] (2)

1a	d2ioha_	A:
1b	d2iohb_	B:
1c	d2iohc_	C:
1d	d2iohd_	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	2iohA01	A:5-23,A:102-260
1b	2iohB01	B:5-23,B:102-260
1c	2iohC01	C:5-23,C:102-260
1d	2iohD01	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	2iohA02	A:24-101
2b	2iohB02	B:24-101
2c	2iohC02	C:24-101
2d	2iohD02	D:24-101

(no "Pfam Domain" information available for 2IOH)

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.

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	2ioh
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	PHNX_BACCE \| O31156	:	1fez 1rdf 1rql 1rqn 1swv 1sww 2iof

2iof	CRYSTAL STRUCTURE OF PHOSPHONOACETALDEHYDE HYDROLASE WITH SODIUM BOROHYDRIDE-REDUCED SUBSTRATE INTERMEDIATE.

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