4UP7 - JenaLib

Title :   CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA LYSYL-TRNA SYNTHETASE IN COMPLEX WITH LYSYL-ADENYLATE

Authors :   L. Bonnefond, O. Nureki

Date :   14 Jun 14 (Deposition) - 29 Oct 14 (Release) - 10 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.79

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

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

Reference :   L. Bonnefond, M. Castro De Moura, L. Ribas De Pouplana, O. Nureki
Crystal Structures Of Entamoeba Histolytica Lysyl-Trna Synthetase Reveal Conformational Changes Upon Lysine Binding And A Specific Helix Bundle Domain.
Febs Lett. V. 588 4478 2014
PubMed-ID: 25448989 | Reference-DOI: 10.1016/J.FEBSLET.2014.10.019

Compounds

Molecule 1 - LYSINE--TRNA LIGASE
	Chains	:	A
	EC Number	:	6.1.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-30 EK/LIC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	C41(DE3) ROSETTA
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ENTAMOEBA HISTOLYTICA
	Organism Taxid	:	5759
	Synonym	:	LYSYL-TRNA SYNTHETASE

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	LAD	1	Ligand/Ion	ADENOSINE-5'-[LYSYL-PHOSPHATE]

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	LAD	2	Ligand/Ion	ADENOSINE-5'-[LYSYL-PHOSPHATE]

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:205 , GLU A:229 , ARG A:251 , GLU A:253 , THR A:258 , HIS A:259 , ASN A:260 , PHE A:263 , THR A:265 , GLU A:267 , TYR A:269 , GLU A:480 , ILE A:481 , ALA A:482 , ASN A:483 , TYR A:485 , GLU A:487 , GLY A:532 , ARG A:539	BINDING SITE FOR RESIDUE LAD A1584

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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

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Chain A from PDB  Type:PROTEIN  Length:529
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh.....ee....eeeeeeeeeeeeee..eeeeeeee..eeeeeeee.hhh.hhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeeeeee..............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...ee.....ee...........eeee....eeeee...hhhhhhhhhhhh..eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhh.....eeeee......eeeee.....eeeehhhhhhhhhh........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...eeee..hhhhh..............eeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhh........hhhhhhhhhh....eeeeeeehhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4up7 A  -6 HHHHHHMLSKQLFLNRCKDVEEYQKAGHNPWPHKFNVSITVPEFIAKYSGLEKSQVSDDIVSVAGRVLSKRSSSSALMFIDLHDSQTKLQIMLNKSAYENKEDFVSLTKMIYRGDICGFTGHPTRTKTGELSLIPISGMILSPCLHMLPSMHYGLGDQETRFRKRYLDLIVNPESVKNFVLRTKVVKAVRKYLDDKGFLEVETPILNTIPGGATARPFITHHNQLDIQMYMRIAPELYLKELVVGGINRVYEIGRLFRNEGIDQTHNPEFTTCEFYMAYADYNDIMKMTEELLGNMVKDITGGSTKLEIKFVTEKKMVLDFTAPFKRISYVHALEEKFGEKIPRPLDGPEALTFLKKQAIRFNAICAEPQTTARVMDKLFGDLIEVDLVQPTFVCDQPQLMSPLAKYHRSEPELTERFELFILKREIANAYTELNNPIVQRSNFEQQAKDKAAGDDEAQLVDEVFLDAIEHAFPPTGGWGLGIDRLAMLLADVDNIKEVILFPTMRPEDELEKKAREAKEDAMVAQELA 583
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303|      374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574         
                                                                                                                                                                                                                                                                                                                                               303|                                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                                                                                365

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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	Cis Peptide Bonds
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		Glu A:422 - Pro A:423	[ RasMol ]
		His A:-6 - His A:-5	[ RasMol ]
		Met A:144 - His A:145	[ RasMol ]
		Thr A:294 - Gly A:295	[ RasMol ]

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

4up8	CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA LYSYL-TRNA SYNTHETASE APO FORM
4up9	CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA LYSYL-TRNA SYNTHETASE IN COMPLEX WITH ATP
4upa	CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA LYSYL-TRNA SYNTHETASE IN COMPLEX WITH AMPPNP

Description