2Z3M - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   COMPLEX STRUCTURE OF LF-TRANSFERASE AND DAF

Authors :   K. Watanabe, Y. Toh, K. Tomita

Date :   04 Jun 07 (Deposition) - 23 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

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

Reference :   K. Watanabe, Y. Toh, K. Suto, Y. Shimizu, N. Oka, T. Wada, K. Tomita
Protein-Based Peptide-Bond Formation By Aminoacyl-Trna Protein Transferase
Nature V. 449 867 2007
PubMed-ID: 17891155 | Reference-DOI: 10.1038/NATURE06167
(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
	Gene	:	AAT
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	L/F-TRANSFERASE, LEUCYLTRANSFERASE, PHENYALANYLTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	3D1	2	Ligand/Ion	(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL
2	PHE	2	Mod. Amino Acid	PHENYLALANINE
3	TAR	2	Ligand/Ion	D(-)-TARTARIC ACID

(no "Site" information available for 2Z3M)

(no "SS Bond" information available for 2Z3M)

Asymmetric/Biological 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 2Z3M)

(no "PROSITE Motif" information available for 2Z3M)

(no "Exon" information available for 2Z3M)

Asymmetric/Biological 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:231
 aligned with LFTR_ECOLI | P0A8P1 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:231
                                    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 RLVQLSRHSIAFPSPEGALREPNGLLALGGDLSPARLLMAYQRGIFPWFSPGDPILWWSPDPRAVLWPESLHISRSMKRFHKRSPYRVTMNYAFGQVIEGCASDREEGTWITRGVVEAYHRLHELGHAHSIEVWREDELVGGMYGVAQGTLFCGESMFSRMENASKTALLVFCEEFIGHGGKLIDCQVLNDHTASLGACEIPRRDYLNYLNQMRLGRLPNNFWVPRCLFSP 232
               SCOP domains d2z3ma_ A: Leucyl/phenylalanyl-tRNA-protein transferase, LFTR (Aat)                                                                                                                                                                     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..hhhhhhh..eeehhhhhhhhhhhhh...........eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3m A   2 RLVQLSRHSIAFPSPEGALREPNGLLALGGDLSPARLLMAYQRGIFPWFSPGDPILWWSPDPRAVLWPESLHISRSMKRFHKRSPYRVTMNYAFGQVIEGCASDREEGTWITRGVVEAYHRLHELGHAHSIEVWREDELVGGMYGVAQGTLFCGESMFSRMENASKTALLVFCEEFIGHGGKLIDCQVLNDHTASLGACEIPRRDYLNYLNQMRLGRLPNNFWVPRCLFSP 232
                                    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:231
 aligned with LFTR_ECOLI | P0A8P1 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:231
                                    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 RLVQLSRHSIAFPSPEGALREPNGLLALGGDLSPARLLMAYQRGIFPWFSPGDPILWWSPDPRAVLWPESLHISRSMKRFHKRSPYRVTMNYAFGQVIEGCASDREEGTWITRGVVEAYHRLHELGHAHSIEVWREDELVGGMYGVAQGTLFCGESMFSRMENASKTALLVFCEEFIGHGGKLIDCQVLNDHTASLGACEIPRRDYLNYLNQMRLGRLPNNFWVPRCLFSP 232
               SCOP domains d2z3mb_ B: Leucyl/phenylalanyl-tRNA-protein transferase, LFTR (Aat)                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------Leu_Phe_trans-2z3mB01 B:34-204                                                                                                                                             ---------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------Leu_Phe_trans-2z3mB02 B:34-204                                                                                                                                             ---------------------------- Pfam domains (2)
         Sec.struct. author ..eee........hhhhh........eee...hhhhhhhhhh...ee........eee....eeeehhhhh..hhhhhhhhhh...eeee..hhhhhhhhhhhh.......hhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhh...eeeee..hhhhhhh..eeehhhhhhhhhhhhh...........eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3m B   2 RLVQLSRHSIAFPSPEGALREPNGLLALGGDLSPARLLMAYQRGIFPWFSPGDPILWWSPDPRAVLWPESLHISRSMKRFHKRSPYRVTMNYAFGQVIEGCASDREEGTWITRGVVEAYHRLHELGHAHSIEVWREDELVGGMYGVAQGTLFCGESMFSRMENASKTALLVFCEEFIGHGGKLIDCQVLNDHTASLGACEIPRRDYLNYLNQMRLGRLPNNFWVPRCLFSP 232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

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/Biological 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: Leucyl/phenylalanyl-tRNA-protein transferase, LFTR (Aat) (7)

Escherichia coli [TaxId: 562] (7)

1a	d2z3ma_	A:
1b	d2z3mb_	B:

(no "CATH Domain" information available for 2Z3M)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Acetyltrans (109)

Family: Leu_Phe_trans (6)

Escherichia coli (strain K12) (6)

1a	Leu_Phe_trans-2z3mB01	B:34-204
1b	Leu_Phe_trans-2z3mB02	B:34-204

Asymmetric/Biological 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/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		3D1	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PHE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TAR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 2z3m)

	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 ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2z3m
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	LFTR_ECOLI \| P0A8P1
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.3.2.6
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	LFTR_ECOLI \| P0A8P1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LFTR_ECOLI \| P0A8P1	:	2cxa 2dps 2dpt 2z3k 2z3l 2z3n 2z3o 2z3p

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File