1WR8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN PH1421 FROM PYROCOCCUS HORIKOSHII.

Authors :   H. Yamamoto, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   13 Oct 04 (Deposition) - 26 Oct 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Alpha / Beta Core Domain, Had Superfamily, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Yamamoto, K. Takio, M. Sugahara, N. Kunishima
Structure Of A Haloacid Dehalogenase Superfamily Phosphatas Ph1421 From Pyrococcus Horikoshii Ot3: Oligomeric State And Thermoadaptation Mechanism.
Acta Crystallogr. , Sect. D V. 64 1068 2008
PubMed-ID: 18931414 | Reference-DOI: 10.1107/S0907444908025948

Molecule 1 - PHOSPHOGLYCOLATE PHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.3.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 11A
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PH1421
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	PGP, HALOACID DEHALOGENASE-LIKE HYDROLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:103 , THR A:105 , ARG A:109 , PHE A:143 , ALA A:144 , HOH A:726 , HOH A:773	BINDING SITE FOR RESIDUE ACT A 600

(no "SS Bond" information available for 1WR8)

(no "Cis Peptide Bond" information available for 1WR8)

(no "SAP(SNP)/Variant" information available for 1WR8)

(no "PROSITE Motif" information available for 1WR8)

(no "Exon" information available for 1WR8)

Asymmetric/Biological 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:230
 aligned with PGP_PYRHO | O50129 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
            PGP_PYRHO     2 KIKAISIDIDGTITYPNRMIHEKALEAIRRAESLGIPIMLVTGNTVQFAEAASILIGTSGPVVAEDGGAISYKKKRIFLASMDEEWILWNEIRKRFPNARTSYTMPDRRAGLVIMRETINVETVREIINELNLNLVAVDSGFAIHVKKPWINKGSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVAVAQAPKILKENADYVTKKEYGEGGAEAIYHILEKFGYL 231
               SCOP domains d1wr8a_ A: Phosphoglycolate phosphatase, PGPase                                                                                                                                                                                        SCOP domains
               CATH domains 1wr8A01 A:2-81,A:151-231  [code=3.40.50.1000, no name defined]                  1wr8A02 A:82-150  [code=3.90.1070.10, no name defined]               1wr8A01 A:2-81,A:151-231  [code=3.40.50.1000, no name defined]                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee............hhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeehhh.eeee..eeee....hhhhhhhhhhhhhh.......hhhhh...eee.....hhhhhhhhhhhh....eeee....eeee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhh...ee...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wr8 A   2 KIKAISIDIDGTITYPNRMIHEKALEAIRRAESLGIPIMLVTGNTVQFAEAASILIGTSGPVVAEDGGAISYKKKRIFLASMDEEWILWNEIRKRFPNARTSYTMPDRRAGLVIMRETINVETVREIINELNLNLVAVDSGFAIHVKKPWINKGSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVAVAQAPKILKENADYVTKKEYGEGGAEAIYHILEKFGYL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

Chain B from PDB  Type:PROTEIN  Length:231
 aligned with PGP_PYRHO | O50129 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
            PGP_PYRHO     1 MKIKAISIDIDGTITYPNRMIHEKALEAIRRAESLGIPIMLVTGNTVQFAEAASILIGTSGPVVAEDGGAISYKKKRIFLASMDEEWILWNEIRKRFPNARTSYTMPDRRAGLVIMRETINVETVREIINELNLNLVAVDSGFAIHVKKPWINKGSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVAVAQAPKILKENADYVTKKEYGEGGAEAIYHILEKFGYL 231
               SCOP domains d1wr8b_ B: Phosphoglycolate phosphatase, PGPase                                                                                                                                                                                         SCOP domains
               CATH domains 1wr8B01 B:1-81,B:151-231  [code=3.40.50.1000, no name defined]                   1wr8B02 B:82-150  [code=3.90.1070.10, no name defined]               1wr8B01 B:1-81,B:151-231  [code=3.40.50.1000, no name defined]                    CATH domains
           Pfam domains (1) -----------------Hydrolase-1wr8B01 B:18-189                                                                                                                                                  ------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------Hydrolase-1wr8B02 B:18-189                                                                                                                                                  ------------------------------------------ Pfam domains (2)
         Sec.struct. author ....eeeee............hhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeehhh.eeee..eeee....hhhhhhhhhhhhhh.......hhhhh...eee.....hhhhhhhhhhhh....eeee....eeee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhhhh.ee...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wr8 B   1 MKIKAISIDIDGTITYPNRMIHEKALEAIRRAESLGIPIMLVTGNTVQFAEAASILIGTSGPVVAEDGGAISYKKKRIFLASMDEEWILWNEIRKRFPNARTSYTMPDRRAGLVIMRETINVETVREIINELNLNLVAVDSGFAIHVKKPWINKGSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVAVAQAPKILKENADYVTKKEYGEGGAEAIYHILEKFGYL 231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: Predicted hydrolases Cof (35)

Protein domain: Phosphoglycolate phosphatase, PGPase (3)

Pyrococcus horikoshii [TaxId: 53953] (1)

1a	d1wr8a_	A:
1b	d1wr8b_	B:

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Hydrolase (64)

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (4)

1a	Hydrolase-1wr8B01	B:18-189
1b	Hydrolase-1wr8B02	B:18-189

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PGP_PYRHO | O50129)

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:0008967	phosphoglycolate phosphatase activity	Catalysis of the reaction: 2-phosphoglycolate + H(2)O = glycolate + phosphate.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.

Asymmetric/Biological Unit
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	1wr8
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (2, 4)

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