1XTY - JenaLib

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Title :   CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS PEPTIDYL-TRNA HYDROLASE

Authors :   M. Fromant, E. Schmitt, Y. Mechulam, C. Lazennec, P. Plateau, S. Blanqu

Date :   25 Oct 04 (Deposition) - 22 Mar 05 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Mixed Beta Sheet, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Fromant, E. Schmitt, Y. Mechulam, C. Lazennec, P. Plateau, S. Blanquet
Crystal Structure At 1. 8 A Resolution And Identification Of Active Site Residues Of Sulfolobus Solfataricus Peptidyl-Trna Hydrolase.
Biochemistry V. 44 4294 2005
PubMed-ID: 15766258 | Reference-DOI: 10.1021/BI047711K

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
	Chains	:	A, B, C, D
	EC Number	:	3.1.1.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-PTHS
	Expression System Strain	:	BL21-ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PTH
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	273057
	Strain	:	DSM1617
	Synonym	:	PTH

		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 (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS D:18 , GLN D:22 , ASP D:86 , ALA D:87 , HOH D:808 , HOH D:835 , HOH D:836 , HOH D:837 , HOH D:842 , HOH D:877 , HOH D:901	BINDING SITE FOR RESIDUE SO4 D 801
2	AC2	SOFTWARE	GLN C:22 , ASP C:86 , ALA C:87 , HOH C:863 , HOH C:864 , HOH C:865 , HOH C:891	BINDING SITE FOR RESIDUE SO4 C 802
3	AC3	SOFTWARE	GLN A:22 , ASP A:86 , ALA A:87 , HOH A:866 , HOH A:889	BINDING SITE FOR RESIDUE SO4 A 803
4	AC4	SOFTWARE	ARG B:9 , HOH B:815	BINDING SITE FOR RESIDUE SO4 B 804
5	AC5	SOFTWARE	HOH A:854 , LYS B:18 , GLN B:22 , ASP B:86 , ALA B:87 , HOH B:841 , HOH B:870 , HOH B:875 , HOH B:889 , HOH B:890 , HOH B:897	BINDING SITE FOR RESIDUE SO4 B 805
6	AC6	SOFTWARE	ARG D:9 , THR D:96 , HOH D:814 , HOH D:917	BINDING SITE FOR RESIDUE SO4 D 806
7	AC7	SOFTWARE	ARG A:9 , HOH A:825 , HOH A:879 , HOH A:880	BINDING SITE FOR RESIDUE SO4 A 807
8	AC8	SOFTWARE	ARG C:9 , THR C:96 , HOH C:828 , HOH C:890 , HOH C:917	BINDING SITE FOR RESIDUE SO4 C 808

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

Asymmetric Unit

No.	Residues
1	Gly A:103	-	Pro A:104
2	Gly B:103	-	Pro B:104
3	Gly C:103	-	Pro C:104
4	Gly D:103	-	Pro D:104

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

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

(no "Exon" information available for 1XTY)

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:120
 aligned with PTH_SULSO | Q980V1 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
            PTH_SULSO     1 MIKMVIVVRSDIKMGKGKIAAQVAHAAVTLVVSIINSNNLRWKEWLNEWLHQGQPKIIVKVNSLDEIISRAKKAETMNLPFSIIEDAGKTQLEPGTITCLGIGPAPENLVDSITGDLKLL 120
               SCOP domains d1xtya_ A: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh...eeeee...........eeeeeeeeeehhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xty A   1 MIKMVIVVRSDIKMGKGKIAAQVAHAAVTLVVSIINSNNLRWKEWLNEWLHQGQPKIIVKVNSLDEIISRAKKAETMNLPFSIIEDAGKTQLEPGTITCLGIGPAPENLVDSITGDLKLL 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with PTH_SULSO | Q980V1 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
            PTH_SULSO     1 MIKMVIVVRSDIKMGKGKIAAQVAHAAVTLVVSIINSNNLRWKEWLNEWLHQGQPKIIVKVNSLDEIISRAKKAETMNLPFSIIEDAGKTQLEPGTITCLGIGPAPENLVDSITGDLKLL 120
               SCOP domains d1xtyb_ B: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh...eeeee...........eeeeeeeeeehhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xty B   1 MIKMVIVVRSDIKMGKGKIAAQVAHAAVTLVVSIINSNNLRWKEWLNEWLHQGQPKIIVKVNSLDEIISRAKKAETMNLPFSIIEDAGKTQLEPGTITCLGIGPAPENLVDSITGDLKLL 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:120
 aligned with PTH_SULSO | Q980V1 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
            PTH_SULSO     1 MIKMVIVVRSDIKMGKGKIAAQVAHAAVTLVVSIINSNNLRWKEWLNEWLHQGQPKIIVKVNSLDEIISRAKKAETMNLPFSIIEDAGKTQLEPGTITCLGIGPAPENLVDSITGDLKLL 120
               SCOP domains d1xtyc_ C: automated matches                                                                                             SCOP domains
               CATH domains 1xtyC00 C:1-120 Bit1                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh...eeeee...........eeeeeeeeeehhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xty C   1 MIKMVIVVRSDIKMGKGKIAAQVAHAAVTLVVSIINSNNLRWKEWLNEWLHQGQPKIIVKVNSLDEIISRAKKAETMNLPFSIIEDAGKTQLEPGTITCLGIGPAPENLVDSITGDLKLL 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:PROTEIN  Length:120
 aligned with PTH_SULSO | Q980V1 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
            PTH_SULSO     1 MIKMVIVVRSDIKMGKGKIAAQVAHAAVTLVVSIINSNNLRWKEWLNEWLHQGQPKIIVKVNSLDEIISRAKKAETMNLPFSIIEDAGKTQLEPGTITCLGIGPAPENLVDSITGDLKLL 120
               SCOP domains d1xtyd_ D: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) PTH2-1xtyD01 D:1-120                                                                                                     Pfam domains (1)
           Pfam domains (2) PTH2-1xtyD02 D:1-120                                                                                                     Pfam domains (2)
           Pfam domains (3) PTH2-1xtyD03 D:1-120                                                                                                     Pfam domains (3)
           Pfam domains (4) PTH2-1xtyD04 D:1-120                                                                                                     Pfam domains (4)
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh...eeeee...........eeeeeeeeeehhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xty D   1 MIKMVIVVRSDIKMGKGKIAAQVAHAAVTLVVSIINSNNLRWKEWLNEWLHQGQPKIIVKVNSLDEIISRAKKAETMNLPFSIIEDAGKTQLEPGTITCLGIGPAPENLVDSITGDLKLL 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

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: Peptidyl-tRNA hydrolase II (9)

Superfamily: Peptidyl-tRNA hydrolase II (9)

Family: automated matches (4)

Protein domain: automated matches (4)

Pyrococcus abyssi [TaxId: 29292] (1)

1a	d1xtya_	A:
1b	d1xtyb_	B:
1c	d1xtyc_	C:
1d	d1xtyd_	D:

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)

Pyrococcus abyssi. Organism_taxid: 29292. Strain: dsm1617. (1)

1xtyC00

C:1-120

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PTH2 (5)

Family: PTH2 (5)

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (1)

1a	PTH2-1xtyD01	D:1-120
1b	PTH2-1xtyD02	D:1-120
1c	PTH2-1xtyD03	D:1-120
1d	PTH2-1xtyD04	D:1-120

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PTH_SULSO | Q980V1)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:103 - Pro A:104	[ RasMol ]
		Gly B:103 - Pro B:104	[ RasMol ]
		Gly C:103 - Pro C:104	[ RasMol ]
		Gly D:103 - Pro D:104	[ RasMol ]

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	1xty
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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