1B70 - JenaLib

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Title :   PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE

Authors :   L. Reshetnikova, N. Moor, O. Lavrik, D. G. Vassylyev

Date :   26 Jan 99 (Deposition) - 09 Feb 00 (Release) - 15 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Enzyme, Trna Synthetase, Dimer Of Alpha/Beta Heterodimers, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Reshetnikova, N. Moor, O. Lavrik, D. G. Vassylyev
Crystal Structures Of Phenylalanyl-Trna Synthetase Complexe With Phenylalanine And A Phenylalanyl-Adenylate Analogue
J. Mol. Biol. V. 287 555 1999
PubMed-ID: 10092459 | Reference-DOI: 10.1006/JMBI.1999.2617
(for further references see the PDB file header)

Molecule 1 - PHENYLALANYL-TRNA SYNTHETASE
	Cellular Location	:	CYTOPLASM
	Chains	:	A
	EC Number	:	6.1.1.20
	Fragment	:	ALPHA SUBUNIT
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	PHERS

Molecule 2 - PHENYLALANYL-TRNA SYNTHETASE
	Cellular Location	:	CYTOPLASM
	Chains	:	B
	EC Number	:	6.1.1.20
	Fragment	:	BETA SUBUNIT
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	PHERS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	PHE	1	Mod. Amino Acid	PHENYLALANINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PHE	2	Mod. Amino Acid	PHENYLALANINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:262 , ASP B:452 , GLU B:461 , GLU B:462	BINDING SITE FOR RESIDUE MG A 351
2	AC2	SOFTWARE	TRP A:149 , HIS A:178 , SER A:180 , ARG A:204 , GLN A:218 , GLU A:220 , PHE A:258 , GLY A:282 , ALA A:283 , ALA A:314 , PHE A:315 , GLY A:316	BINDING SITE FOR RESIDUE PHE A 352

(no "SS Bond" information available for 1B70)

Asymmetric Unit

No.	Residues
1	Pro A:192	-	Pro A:193
2	Gly A:246	-	Pro A:247
3	Glu A:262	-	Pro A:263
4	Gly B:439	-	Pro B:440
5	Leu B:675	-	Pro B:676

(no "SAP(SNP)/Variant" information available for 1B70)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRBD	PS50886	tRNA-binding domain profile.	SYFB_THETH	39-147	1	B:39-147
2	B5	PS51483	B5 domain profile.	SYFB_THETH	399-474	1	B:399-474
3	FDX_ACB	PS51447	Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.	SYFB_THETH	688-780	1	B:688-775

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRBD	PS50886	tRNA-binding domain profile.	SYFB_THETH	39-147	2	B:39-147
2	B5	PS51483	B5 domain profile.	SYFB_THETH	399-474	2	B:399-474
3	FDX_ACB	PS51447	Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.	SYFB_THETH	688-780	2	B:688-775

(no "Exon" information available for 1B70)

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:265
 aligned with SYFA_THETH | P27001 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:265
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345     
           SYFA_THETH    86 VDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVEGPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTPPFRIVVPGRVFRFEQTDATHEAVFHQLEGLVVGEGIAMAHLKGAIYELAQALFGPDSKVRFQPVYFPFVEPGAQFAVWWPEGGKWLELGGAGMVHPKVFQAVDAYRERLGLPPAYRGVTGFAFGLGVERLAMLRYGIPDIRYFFGGRLKFLEQFKGVL 350
               SCOP domains d1b70a_ A: Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS                                                                                                                                                                                                             SCOP domains
               CATH domains 1b70A00 A:86-350 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhh...ee.....eeehhhhh..........hhhhh....ee.................eee....hhhhhhhhhhh...eeeeeeeeee...........eeeeeeeeeee...hhhhhhhhhhhhhhhhh.....eeeee.....eeeeeeeeeee....eeeeeeeeeeehhhhhhhhhhhhhhh.........eeeeeeeehhhhhhhhhh..hhhhhhh.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b70 A  86 VDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVEGPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTPPFRIVVPGRVFRFEQTDATHEAVFHQLEGLVVGEGIAMAHLKGAIYELAQALFGPDSKVRFQPVYFPFVEPGAQFAVWWPEGGKWLELGGAGMVHPKVFQAVDAYRERLGLPPAYRGVTGFAFGLGVERLAMLRYGIPDIRYFFGGRLKFLEQFKGVL 350
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

Chain B from PDB  Type:PROTEIN  Length:775
 aligned with SYFB_THETH | P27002 from UniProtKB/Swiss-Prot  Length:785

    Alignment length:775
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770     
           SYFB_THETH     1 MRVPFSWLKAYVPELESPEVLEERLAGLGFETDRIERVFPIPRGVVFARVLEAHPIPGTRLKRLVLDAGRTVEVVSGAENARKGIGVALALPGTELPGLGQKVGERVIQGVRSFGMALSPRELGVGEYGGGLLEFPEDALPPGTPLSEAWPEEVVLDLEVTPNRPDALGLLGLARDLHALGYALVEPEAALKAEALPLPFALKVEDPEGAPHFTLGYAFGLRVAPSPLWMQRALFAAGMRPINNVVDVTNYVMLERAQPMHAFDLRFVGEGIAVRRAREGERLKTLDGVERTLHPEDLVIAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHRFERGVDPLGQVPAQRRALSLLQALAGARVAEALLEAGSPKPPEAIPFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVTPPSHRLDLRLEEDLVEEVARIQGYETIPLALPAFFPAPDNRGVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDARRFRLDPPRLLLLNPLAPEKAALRTHLFPGLVRVLKENLDLDRPERALLFEVGRVFREREETHLAGLLFGEGVGLPWAKERLSGYFLLKGYLEALFARLGLAFRVEAQAFPFLHPGVSGRVLVEGEEVGFLGALHPEIAQELELPPVHLFELRLPLPDKPLAFQDPSRHPAAFRDLAVVVPAPTPYGEVEALVREAAGPYLESLALFDLYQGPPLPEGHKSLAFHLRFRHPKRTLRDEEVEEAVSRVAEALRAR 775
               SCOP domains d1b70b1 B:1-38,B:152-190              d1b70b3 B:39-151 Domain B2 of PheRS-beta, PheT                                                                   d1b70b1 B:1-38,B:152-190               d1b70b6 B:191-399 B3/B4 domain of PheRS, PheT                                                                                                                                                                    d1b70b2 B:400-474 Domains B1 and B5 of PheRS-beta, PheT                    d1b70b5 B:475-681 Phenyl-tRNA synthetase (PheRS) beta subunit, PheT, central domain                                                                                                                            d1b70b4 B:682-775 Phenylalanyl-tRNA synthetase                                                 SCOP domains
               CATH domains 1b70B01 B:1-37,B:154-186             1b70B02 B:38-153 Nucleic acid-binding proteins                                                                      1b70B01 B:1-37,B:154-186         1b70B03 B:187-400 Phenylalanyl-trna Synthetase, Chain B, domain 3                                                                                                                                                     1b70B04 B:401-474  [code=3.30.56.20, no name defined]                     --------------1b70B05 B:489-679 Bira Bifunctional Protein; Domain 2                                                                                                                                          ----------1b70B06 B:690-775  [code=3.30.70.380, no name defined]                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhh......hhhhhhhhhhhhh..eeeeee.......eeeeeeeeeeee....eeeeeee...eeeeee.........eeeee...............ee....ee..ee.hhhhhh....................hhhhh....eeeee.....hhhhhhhhhhhhhhhhh............ee......eeee.......eeeeeeee.......hhhhhhhhhhh.....hhhhhhhhhhhhhh...eeeee.hhh..eeeeee.....eee.....eee.....eeeeeee..eeeeeee...ee...........eeeeeeee.hhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhh..eee...eee........eeehhhhhhhhhh...hhhhhhhhhhhh..eee.....eeee.........hhhhhhhhhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhh.ee.....ee..hhhhhh.......ee....hhhhhee...hhhhhhhhhhhhhhhh....eeeeeeeeee...eeeeeeeeee...ee......ee.hhhhhhhhhhhhhhhhh...eee.............eeee..eeeeeeee.hhhhhhhh.....eeeeeee.................eeeee...ee...hhhhhhhhhhhhh...eeeeeeee..........ee..eeeeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------TRBD  PDB: B:39-147 UniProt: 39-147                                                                          -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------B5  PDB: B:399-474 UniProt: 399-474                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FDX_ACB  PDB: B:688-775 UniProt: 688-780                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b70 B   1 MRVPFSWLKAYVPELESPEVLEERLAGLGFETDRIERVFPIPRGVVFARVLEAHPIPGTRLKRLVLDAGRTVEVVSGAENARKGIGVALALPGTELPGLGQKVGERVIQGVRSFGMALSPRELGVGEYGGGLLEFPEDALPPGTPLSEAWPEEVVLDLEVTPNRPDALGLLGLARDLHALGYALVEPEAALKAEALPLPFALKVEDPEGAPHFTLGYAFGLRVAPSPLWMQRALFAAGMRPINNVVDVTNYVMLERAQPMHAFDLRFVGEGIAVRRAREGERLKTLDGVERTLHPEDLVIAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHRFERGVDPLGQVPAQRRALSLLQALAGARVAEALLEAGSPKPPEAIPFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVTPPSHRLDLRLEEDLVEEVARIQGYETIPLALPAFFPAPDNRGVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDARRFRLDPPRLLLLNPLAPEKAALRTHLFPGLVRVLKENLDLDRPERALLFEVGRVFREREETHLAGLLFGEGVGLPWAKERLSGYFLLKGYLEALFARLGLAFRVEAQAFPFLHPGVSGRVLVEGEEVGFLGALHPEIAQELELPPVHLFELRLPLPDKPLAFQDPSRHPAAFRDLAVVVPAPTPYGEVEALVREAAGPYLESLALFDLYQGPPLPEGHKSLAFHLRFRHPKRTLRDEEVEEAVSRVAEALRAR 775
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770

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 '\|'

(no "Pfam Domain" information available for 1B70)

Asymmetric Unit(hide GO term definitions)

Chain A (SYFA_THETH | P27001)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004812	aminoacyl-tRNA ligase activity	Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004826	phenylalanine-tRNA ligase activity	Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0006432	phenylalanyl-tRNA aminoacylation	The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
	GO:0043039	tRNA aminoacylation	The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
	GO:0006418	tRNA aminoacylation for protein translation	The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
	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.

Chain B (SYFB_THETH | P27002)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004812	aminoacyl-tRNA ligase activity	Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004826	phenylalanine-tRNA ligase activity	Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0006432	phenylalanyl-tRNA aminoacylation	The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
	GO:0043039	tRNA aminoacylation	The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	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
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		Gly A:246 - Pro A:247	[ RasMol ]
		Gly B:439 - Pro B:440	[ RasMol ]
		Leu B:675 - Pro B:676	[ RasMol ]
		Pro A:192 - Pro A:193	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1B70)

Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

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