4DHW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM PSEUDOMONAS AERUGINOSA WITH ADIPIC ACID AT 2.4 ANGSTROM RESOLUTION

Authors :   A. Kumar, A. Singh, N. Singh, M. Sinha, S. Sharma, A. Arora, T. P. Singh

Date :   30 Jan 12 (Deposition) - 29 Feb 12 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.43

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

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

Reference :   A. Kumar, A. Singh, N. Singh, M. Sinha, S. Sharma, A. Arora, T. P. Singh
Crystal Structure Of Peptidyl-Trna Hydrolase From Pseudomonas Aeruginosa With Adipic Acid At 2. 4 Angstrom Resolution
To Be Published
PubMed: search

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
	Chains	:	A, B
	EC Number	:	3.1.1.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-NH6
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PA4672, PTH
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208964
	Strain	:	ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228
	Synonym	:	PTH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	0L1	2	Ligand/Ion	HEXANEDIOIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	0L1	1	Ligand/Ion	HEXANEDIOIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	0L1	1	Ligand/Ion	HEXANEDIOIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:22 , ASP A:95 , GLU A:96 , LEU A:97 , GLY A:114 , HIS A:115 , ASN A:116 , HOH A:339 , HOH A:364	BINDING SITE FOR RESIDUE 0L1 A 201
2	AC2	SOFTWARE	HIS B:22 , ASP B:95 , GLU B:96 , LEU B:97 , GLY B:114 , HIS B:115 , ASN B:116 , VAL B:151 , HOH B:362	BINDING SITE FOR RESIDUE 0L1 B 201

(no "SS Bond" information available for 4DHW)

(no "Cis Peptide Bond" information available for 4DHW)

(no "SAP(SNP)/Variant" information available for 4DHW)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPT_TRNA_HYDROL_1	PS01195	Peptidyl-tRNA hydrolase signature 1.	PTH_PSEAE	17-30	2	A:17-30 B:17-30
2	PEPT_TRNA_HYDROL_2	PS01196	Peptidyl-tRNA hydrolase signature 2.	PTH_PSEAE	111-121	2	A:111-121 B:111-121

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPT_TRNA_HYDROL_1	PS01195	Peptidyl-tRNA hydrolase signature 1.	PTH_PSEAE	17-30	1	A:17-30 -
2	PEPT_TRNA_HYDROL_2	PS01196	Peptidyl-tRNA hydrolase signature 2.	PTH_PSEAE	111-121	1	A:111-121 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPT_TRNA_HYDROL_1	PS01195	Peptidyl-tRNA hydrolase signature 1.	PTH_PSEAE	17-30	1	- B:17-30
2	PEPT_TRNA_HYDROL_2	PS01196	Peptidyl-tRNA hydrolase signature 2.	PTH_PSEAE	111-121	1	- B:111-121

(no "Exon" information available for 4DHW)

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:194
 aligned with PTH_PSEAE | Q9HVC3 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
            PTH_PSEAE     1 MTAVQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDIIAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGDWTRAMQKLHSQKA 194
               SCOP domains d4dhwa_ A: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..........hhhhhhhhhhhhhhhhh....eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PEPT_TRNA_HYDR--------------------------------------------------------------------------------PEPT_TRNA_H------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dhw A   1 MTAVQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDIIAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGDWTRAMQKLHSQKA 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:194
 aligned with PTH_PSEAE | Q9HVC3 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
            PTH_PSEAE     1 MTAVQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDIIAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGDWTRAMQKLHSQKA 194
               SCOP domains d4dhwb_ B: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..........hhhhhhhhhhhhhhhhhh...eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PEPT_TRNA_HYDR--------------------------------------------------------------------------------PEPT_TRNA_H------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dhw B   1 MTAVQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDIIAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGDWTRAMQKLHSQKA 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Phosphorylase/hydrolase-like (558)

Superfamily: Peptidyl-tRNA hydrolase-like (33)

Family: automated matches (29)

Protein domain: automated matches (29)

Pseudomonas aeruginosa [TaxId: 208964] (6)

1a	d4dhwa_	A:
1b	d4dhwb_	B:

(no "CATH Domain" information available for 4DHW)

(no "Pfam Domain" information available for 4DHW)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTH_PSEAE | Q9HVC3)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dhw)

Biological Units
	Complete Structure
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		Biological Unit 2	[ Jena3D ]

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	3.1.1.29
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	PTH_PSEAE \| Q9HVC3	:	4djj 4erx 4fno 4fyj 4jc4 4qaj 4qbk 4qd3

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