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Description

Title :   STRUCTURE OF CONSERVED PROTEIN OF UNKNOWN FUNCTION TA0108 FROM THERMOPLASMA ACIDOPHILUM

Authors :   J. Osipiuk, E. Evdokimova, A. Savchenko, A. Edwards, A. Joachimiak, Mi Center For Structural Genomics (Mcsg)

Date :   25 Nov 03 (Deposition) - 30 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

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

Reference :   J. Osipiuk, E. Evdokimova, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of Conserved Hypothetical Protein Ta0108 From Thermoplasma Acidophilum
To Be Published
PubMed: search

Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TA0108
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TA0108
	Organism Scientific	:	THERMOPLASMA ACIDOPHILUM
	Organism Taxid	:	2303

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:19 , GLN A:23 , HIS A:26 , ARG A:52 , ASP A:83 , ARG A:84 , HOH A:317 , HOH A:322 , HOH A:334	BINDING SITE FOR RESIDUE SO4 A 201
2	AC2	SOFTWARE	GLY A:18 , LYS A:19 , ALA A:22 , LYS A:53 , ILE A:54 , VAL A:55 , LEU A:116 , LEU A:117	BINDING SITE FOR RESIDUE GOL A 301

SS Bonds (0, 0)

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

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Gly A:100	-	Pro A:101

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (0, 0)

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

Exons (0, 0)

(no "Exon" information available for 1RLK)

Sequences/Alignments

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:116
 aligned with PTH_THEAC | Q9HLW6 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:116
                                    11        21        31        41        51        61        71        81        91       101       111      
            PTH_THEAC     2 VKKMVIAVRKDLDMGKGKIAAQVAHAAVTCAIRSMKINRDVFNEWYDEGQRKIVVKVNDLDEIMEIKRMADSMGIVNEIVQDRGYTQVEPGTITCIGLGPDEEEKLDKITGKYKLL 117
               SCOP domains d1rlka_ A: Hypothetical protein TA0108                                                                               SCOP domains
               CATH domains 1rlkA00 A:2-117 Bit1                                                                                                 CATH domains
               Pfam domains PTH2-1rlkA01 A:2-117                                                                                                 Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh..eeeee...........eeeeeeeeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1rlk A   2 VKKMVIAVRKDLDMGKGKIAAQVAHAAVTCAIRSMKINRDVFNEWYDEGQRKIVVKVNDLDEIMEIKRMADSMGIVNEIVQDRGYTQVEPGTITCIGLGPDEEEKLDKITGKYKLL 117
                                    11        21        31        41        51        61        71        81        91       101       111

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Peptidyl-tRNA hydrolase II (9)

Superfamily: Peptidyl-tRNA hydrolase II (9)

Family: Peptidyl-tRNA hydrolase II (5)

Protein domain: Hypothetical protein TA0108 (1)

Thermoplasma acidophilum [TaxId: 2303] (1)

d1rlka_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Bit1 (5)

Homologous Superfamily: Bit1 (5)

Thermoplasma acidophilum. Organism_taxid: 2303. (1)

1rlkA00

A:2-117

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PTH2 (5)

Family: PTH2 (5)

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

PTH2-1rlkA01

A:2-117

Gene Ontology (4, 4)

Asymmetric Unit(hide GO term definitions)

Chain A (PTH_THEAC | Q9HLW6)

molecular function
	GO:0004045	aminoacyl-tRNA hydrolase activity	Catalysis of the reaction: N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA.
	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.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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Description

Compounds

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