1KYT - JenaLib

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Title :   CRYSTAL STRUCTURE OF THERMOPLASMA ACIDOPHILUM 0175 (APC014)

Authors :   Y. Kim, A. Joachimiak, A. Edwards, X. Xu, M. Pennycooke, J. Gu, F. Cheung D. Christendat, Midwest Center For Structural Genomics (Mcsg)

Date :   05 Feb 02 (Deposition) - 21 Jan 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Structural Genomics, Putative Hydrolase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, A. Joachimiak, A. Edwards, X. Xu, M. Pennycooke, J. Gu, F. Cheung, D. Christendat
Crystal Structure Of Thermoplasma Acidophilum 0175 (Apc014)
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN TA0175
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TA0175
	Mutation	:	YES
	Organism Scientific	:	THERMOPLASMA ACIDOPHILUM
	Organism Taxid	:	2303

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 24)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 18)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 9)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:8 , ASP B:10 , ASP B:174 , SER B:175 , ASP B:178 , HOH B:508 , HOH B:510	BINDING SITE FOR RESIDUE CA B 501
2	AC2	SOFTWARE	ASP A:8 , ASP A:174 , SER A:175 , ASN A:177 , ASP A:178 , HOH A:534 , HOH A:567	BINDING SITE FOR RESIDUE CA A 502
3	AC3	SOFTWARE	GLY A:11 , ASP A:174 , HOH A:514 , HOH A:524 , HOH A:530 , HOH A:532 , HOH A:538	BINDING SITE FOR RESIDUE CA A 503
4	AC4	SOFTWARE	GLU A:119 , GLY B:139 , HOH B:505 , HOH B:633 , HOH B:634 , HOH B:635	BINDING SITE FOR RESIDUE CA B 504
5	AC5	SOFTWARE	ASN A:44 , SER A:138 , TYR A:140 , HOH A:537	BINDING SITE FOR RESIDUE CA A 505
6	AC6	SOFTWARE	HOH A:583 , HOH A:642	BINDING SITE FOR RESIDUE CA A 506

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

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

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

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

(no "Exon" information available for 1KYT)

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:225
 aligned with PGP_THEAC | Q9HLQ2 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:225
                             1                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
            PGP_THEAC     - -MIRLAAIDVDGTLTDRDRLISTKAIESIRSAEKKGLTVSLLSGNVIPVVYALKIFLGINGPVFGENGGIMFDNDGSIKKFFSNEGTNKFLEEMSKRTSMRSILTNRWREASTGFDIDPEDVDYVRKEAESRGFVIFYSGYSWHLMNRGEDKAFAVNKLKEMYSLEYDEILVIGDSNNDMPMFQLPVRKACPANATDNIKAVSDFVSDYSYGEEIGQIFKHFELM 224
               SCOP domains d1kyta_ A: Phosphoglycolate phosphatase, PGPase                                                                                                                                                                                   SCOP domains
               CATH domains --1kytA01 A:2-80,A:146-223  [code=3.40.50.1000, no name defined]                 1kytA02 A:81-144  [code=3.90.1070.10, no name defined]          -1kytA01 A:2-80,A:146-223  [code=3.40.50.1000, no name defined]                - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhh.......hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh....eeehhh.eee.....eee...hhhhhhhhhhhh.......hhhhhhh...eee..hhhhhhhhhhhhhhh.eeeeee..eeeeee...hhhhhhhhhhhhh..hhh.eeee..hhhhhhhhh...eeee....hhhhhhhh.ee......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyt A   0 HmIRLAAIDVDGNLTDRDRLISTKAIESIRSAEKKGLTVSLLSGNVIPVVYALKIFLGINGPVFGENGGImFDNDGSIKKFFSNEGTNKFLEEmSKRTSmRSILTNRWREASTGFDIDPEDVDYVRKEAESRGFVIFYSGYSWHLmNRGEDKAFAVNKLKEmYSLEYDEILVIGDSNNDmPmFQLPVRKACPANATDNIKAVSDFVSDYSYGEEIGQIFKHFELm 224
                             |       9        19        29        39        49        59        69|       79        89   |    99       109       119       129       139     | 149       159 |     169       179 |     189       199       209       219    |
                             |                                                                   70-MSE                 93-MSE |                                           145-MSE         161-MSE           179-MSE                                      224-MSE
                             1-MSE                                                                                            99-MSE                                                                           181-MSE

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with PGP_THEAC | Q9HLQ2 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:225
                             1                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
            PGP_THEAC     - -MIRLAAIDVDGTLTDRDRLISTKAIESIRSAEKKGLTVSLLSGNVIPVVYALKIFLGINGPVFGENGGIMFDNDGSIKKFFSNEGTNKFLEEMSKRTSMRSILTNRWREASTGFDIDPEDVDYVRKEAESRGFVIFYSGYSWHLMNRGEDKAFAVNKLKEMYSLEYDEILVIGDSNNDMPMFQLPVRKACPANATDNIKAVSDFVSDYSYGEEIGQIFKHFELM 224
               SCOP domains d1kytb_ B: Phosphoglycolate phosphatase, PGPase                                                                                                                                                                                   SCOP domains
               CATH domains --1kytB01 B:2-80,B:146-223  [code=3.40.50.1000, no name defined]                 1kytB02 B:81-144  [code=3.90.1070.10, no name defined]          -1kytB01 B:2-80,B:146-223  [code=3.40.50.1000, no name defined]                - CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------Hydrolase_3-1kytB01 B:102-216                                                                                      -------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------Hydrolase_3-1kytB02 B:102-216                                                                                      -------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------Hydrolase_3-1kytB03 B:102-216                                                                                      -------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------Hydrolase_3-1kytB04 B:102-216                                                                                      -------- Pfam domains (4)
         Sec.struct. author ....eeeee............hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh....eeehhh.eee.....eee...hhhhhhhhhhhh.......hhhhhhh...eee..hhhhhhhhhhhhhh..eeeeee..eeeeee...hhhhhhhhhhhhhh.hhh.eeee..hhhhhhhhh...eeee....hhhhhhhh.ee.....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyt B   0 HmIRLAAIDVDGNLTDRDRLISTKAIESIRSAEKKGLTVSLLSGNVIPVVYALKIFLGINGPVFGENGGImFDNDGSIKKFFSNEGTNKFLEEmSKRTSmRSILTNRWREASTGFDIDPEDVDYVRKEAESRGFVIFYSGYSWHLmNRGEDKAFAVNKLKEmYSLEYDEILVIGDSNNDmPmFQLPVRKACPANATDNIKAVSDFVSDYSYGEEIGQIFKHFELm 224
                             |       9        19        29        39        49        59        69|       79        89   |    99       109       119       129       139     | 149       159 |     169       179 |     189       199       209       219    |
                             |                                                                   70-MSE                 93-MSE |                                           145-MSE         161-MSE           179-MSE                                      224-MSE
                             1-MSE                                                                                            99-MSE                                                                           181-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: 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)

Thermoplasma acidophilum [TaxId: 2303] (2)

1a	d1kyta_	A:
1b	d1kytb_	B:

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)

Thermoplasma acidophilum. Organism_taxid: 2303. (3)

1a	1kytA01	A:2-80,A:146-223
1b	1kytB01	B:2-80,B:146-223

Architecture: Alpha-Beta Complex (3881)

Topology: Hypothetical Protein Ta0175; Chain: A, domain 2 (12)

Homologous Superfamily: [code=3.90.1070.10, no name defined] (12)

Thermoplasma acidophilum. Organism_taxid: 2303. (2)

2a	1kytA02	A:81-144
2b	1kytB02	B:81-144

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Hydrolase_3 (28)

Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (1)

1a	Hydrolase_3-1kytB01	B:102-216
1b	Hydrolase_3-1kytB02	B:102-216
1c	Hydrolase_3-1kytB03	B:102-216
1d	Hydrolase_3-1kytB04	B:102-216

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGP_THEAC | Q9HLQ2)

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 Unit
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Description

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Ligands, Modified Residues, Ions (2, 24)

Sites (6, 6)

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