2DPT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   LEUCYL/PHENYLALANYL-TRNA-PROTEIN TRANSFERASE COMPLEXED WITH PUROMYCIN

Authors :   K. Suto, Y. Shimizu, K. Tomita

Date :   14 May 06 (Deposition) - 02 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   Aminoacyl-Trna-Protein Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Suto, Y. Shimizu, K. Watanabe, T. Ueda, S. Fukai, O. Nureki, K. Tomita
Crystal Structures Of Leucyl/Phenylalanyl-Trna-Protein Transferase And Its Complex With An Aminoacyl-Trna Analog
Embo J. V. 25 5942 2006
PubMed-ID: 17110926 | Reference-DOI: 10.1038/SJ.EMBOJ.7601433
(for further references see the PDB file header)

Molecule 1 - LEUCYL/PHENYLALANYL-TRNA--PROTEIN TRANSFERASE
	Chains	:	A, B
	EC Number	:	2.3.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	L/F-TRANSFERASE, LEUCYLTRANSFERASE, PHENYALANYLTRANSFERASE

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	PUY	2	Ligand/Ion	PUROMYCIN
2	TAR	2	Ligand/Ion	D(-)-TARTARIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	PUY	1	Ligand/Ion	PUROMYCIN
2	TAR	1	Ligand/Ion	D(-)-TARTARIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	PUY	1	Ligand/Ion	PUROMYCIN
2	TAR	1	Ligand/Ion	D(-)-TARTARIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:47 , TRP A:49 , TRP A:59 , GLU A:108 , MET A:144 , PHE A:153 , GLY A:155 , GLU A:156 , SER A:157 , MET A:158 , ILE A:185 , CYS A:187 , GLN A:188 , VAL A:189 , ASN A:191	BINDING SITE FOR RESIDUE PUY A 501
2	AC2	SOFTWARE	TRP B:49 , TRP B:59 , MET B:144 , PHE B:153 , GLY B:155 , GLU B:156 , SER B:157 , CYS B:187 , GLN B:188 , ASN B:191 , HOH B:1001	BINDING SITE FOR RESIDUE PUY B 1501
3	AC3	SOFTWARE	SER A:160 , GLU A:163 , ASN A:164 , ALA A:165 , SER A:166 , LYS A:167	BINDING SITE FOR RESIDUE TAR A 502
4	AC4	SOFTWARE	SER B:160 , GLU B:163 , ASN B:164 , ALA B:165 , SER B:166 , LYS B:167	BINDING SITE FOR RESIDUE TAR B 1502

(no "SS Bond" information available for 2DPT)

Asymmetric Unit

No.	Residues
1	Glu A:22	-	Pro A:23
2	Asp A:62	-	Pro A:63
3	Glu B:22	-	Pro B:23
4	Asp B:62	-	Pro B:63

(no "SAP(SNP)/Variant" information available for 2DPT)

(no "PROSITE Motif" information available for 2DPT)

(no "Exon" information available for 2DPT)

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:232
 aligned with LFTR_ECOLI | P0A8P1 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
           LFTR_ECOLI     2 RLVQLSRHSIAFPSPEGALREPNGLLALGGDLSPARLLMAYQRGIFPWFSPGDPILWWSPDPRAVLWPESLHISRSMKRFHKRSPYRVTMNYAFGQVIEGCASDREEGTWITRGVVEAYHRLHELGHAHSIEVWREDELVGGMYGVAQGTLFCGESMFSRMENASKTALLVFCEEFIGHGGKLIDCQVLNDHTASLGACEIPRRDYLNYLNQMRLGRLPNNFWVPRCLFSPQ 233
               SCOP domains d2dpta_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........hhhhh......eeeee...hhhhhhhhhhh..ee........eee....eeeehhhhh..hhhhhhhhhh...eeee..hhhhhhhhhh.........hhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhh...eeeee..hhhhhhh..eeehhhhhhhhhhhhh...........eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpt A   2 RLVQLSRHSIAFPSPEGALREPNGLLALGGDLSPARLLMAYQRGIFPWFSPGDPILWWSPDPRAVLWPESLHISRSMKRFHKRSPYRVTMNYAFGQVIEGCASDREEGTWITRGVVEAYHRLHELGHAHSIEVWREDELVGGMYGVAQGTLFCGESMFSRMENASKTALLVFCEEFIGHGGKLIDCQVLNDHTASLGACEIPRRDYLNYLNQMRLGRLPNNFWVPRCLFSPQ 233
                                    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:232
 aligned with LFTR_ECOLI | P0A8P1 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  
           LFTR_ECOLI     1 MRLVQLSRHSIAFPSPEGALREPNGLLALGGDLSPARLLMAYQRGIFPWFSPGDPILWWSPDPRAVLWPESLHISRSMKRFHKRSPYRVTMNYAFGQVIEGCASDREEGTWITRGVVEAYHRLHELGHAHSIEVWREDELVGGMYGVAQGTLFCGESMFSRMENASKTALLVFCEEFIGHGGKLIDCQVLNDHTASLGACEIPRRDYLNYLNQMRLGRLPNNFWVPRCLFSP 232
               SCOP domains d2dptb_ B: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee........hhhhh......eeeee...hhhhhhhhhhh..ee........eee....eeeehhhhh..hhhhhhhhhh...eeee..hhhhhhhhhhhh.......hhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhh...eeeee..hhhhhh...eeehhhhhhhhhhhhh...........eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpt B   1 MRLVQLSRHSIAFPSPEGALREPNGLLALGGDLSPARLLMAYQRGIFPWFSPGDPILWWSPDPRAVLWPESLHISRSMKRFHKRSPYRVTMNYAFGQVIEGCASDREEGTWITRGVVEAYHRLHELGHAHSIEVWREDELVGGMYGVAQGTLFCGESMFSRMENASKTALLVFCEEFIGHGGKLIDCQVLNDHTASLGACEIPRRDYLNYLNQMRLGRLPNNFWVPRCLFSP 232
                                    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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Acyl-CoA N-acyltransferases (Nat) (250)

Superfamily: Acyl-CoA N-acyltransferases (Nat) (250)

Family: LFTR-like (9)

Protein domain: automated matches (2)

Escherichia coli [TaxId: 562] (2)

1a	d2dpta_	A:
1b	d2dptb_	B:

(no "CATH Domain" information available for 2DPT)

(no "Pfam Domain" information available for 2DPT)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LFTR_ECOLI | P0A8P1)

molecular function
	GO:0008914	leucyltransferase activity	Catalysis of the reaction: L-leucyl-tRNA + protein = tRNA + L-leucyl-protein.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
	GO:0016755	transferase activity, transferring amino-acyl groups	Catalysis of the transfer of an amino-acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0030163	protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
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
		Asp A:62 - Pro A:63	[ RasMol ]
		Asp B:62 - Pro B:63	[ RasMol ]
		Glu A:22 - Pro A:23	[ RasMol ]
		Glu B:22 - Pro B:23	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	2dpt
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	2.3.2.6
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	LFTR_ECOLI \| P0A8P1	:	2cxa 2dps 2z3k 2z3l 2z3m 2z3n 2z3o 2z3p

2dps	THE NATIVE FORM OF THE SAME PROTEIN

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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