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(-) Description

Title :  CRYSTAL STRUCTURE OF T.THERMOPHILUS PHENYLALANYL-TRNA SYNTHETASE COMPLEXED WITH P-CL-PHENYLALANINE
 
Authors :  O. M. Kotik-Kogan, N. A. Moor, D. E. Tworowski, M. G. Safro
Date :  04 Aug 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Protein-Unnatural Amino Acid Complex, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. M. Kotik-Kogan, N. A. Moor, D. E. Tworowski, M. G. Safro
Structural Basis For Discrimination Of L-Phenylalanine From L-Tyrosine By Phenylalanyl-Trna Synthetase
Structure V. 13 1799 2005
PubMed-ID: 16338408  |  Reference-DOI: 10.1016/J.STR.2005.08.013

(-) Compounds

Molecule 1 - PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN
    ChainsA
    EC Number6.1.1.20
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    Other DetailsGENE PHES
    StrainHB8
    SynonymPHENYLALANINE--TRNA LIGASE ALPHA CHAIN;
PHERS
 
Molecule 2 - PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN
    ChainsB
    EC Number6.1.1.20
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    Other DetailsGENE PHET
    StrainHB8
    SynonymPHENYLALANINE--TRNA LIGASE BETA CHAIN;
PHERS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
12001Ligand/Ion4-CHLORO-L-PHENYLALANINE
2MN1Ligand/IonMANGANESE (II) ION
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
12002Ligand/Ion4-CHLORO-L-PHENYLALANINE
2MN-1Ligand/IonMANGANESE (II) ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:262 , ASP B:452 , GLU B:461BINDING SITE FOR RESIDUE MN A 901
2AC2SOFTWAREARG B:407 , ARG B:413BINDING SITE FOR RESIDUE SO4 B 786
3AC3SOFTWARETRP A:149 , HIS A:178 , SER A:180 , ARG A:204 , GLN A:218 , GLU A:220 , PHE A:258 , PHE A:260 , VAL A:261 , ALA A:283 , ALA A:314 , PHE A:315 , GLY A:316BINDING SITE FOR RESIDUE 200 A 999

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Pro A:192 -Pro A:193
2Glu A:262 -Pro A:263
3Gly B:439 -Pro B:440
4Leu B:675 -Pro B:676
5Pro B:734 -Pro B:735

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRBDPS50886 tRNA-binding domain profile.SYFB_THETH39-147  1B:39-147
2B5PS51483 B5 domain profile.SYFB_THETH399-474  1B:399-474
3FDX_ACBPS51447 Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.SYFB_THETH688-780  1B:688-780
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRBDPS50886 tRNA-binding domain profile.SYFB_THETH39-147  2B:39-147
2B5PS51483 B5 domain profile.SYFB_THETH399-474  2B:399-474
3FDX_ACBPS51447 Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.SYFB_THETH688-780  2B:688-780

(-) Exons   (0, 0)

(no "Exon" information available for 2AKW)

(-) 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    
   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:266
 aligned with SYFA_THETH | P27001 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:266
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344      
           SYFA_THETH    85 RVDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVEGPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTPPFRIVVPGRVFRFEQTDATHEAVFHQLEGLVVGEGIAMAHLKGAIYELAQALFGPDSKVRFQPVYFPFVEPGAQFAVWWPEGGKWLELGGAGMVHPKVFQAVDAYRERLGLPPAYRGVTGFAFGLGVERLAMLRYGIPDIRYFFGGRLKFLEQFKGVL 350
               SCOP domains d2akwa_ A: Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS                                                                                                                                                                                                              SCOP domains
               CATH domains 2akwA00 A:85-350 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhh...ee.....eeehhhhhhhhh....hhhhhhh..eeee.................eee....hhhhhhhhhhh...eeeeeeeeee...........eeeeeeeeeee...hhhhhhhhhhhhhhhhhh....eeee......eeeeeeeeeee....eeeeeeeeeeehhhhhhhhhhhhhhh.........eeeeeeeehhhhhhhhhh..hhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2akw A  85 RVDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVEGPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTPPFRIVVPGRVFRFEQTDATHEAVFHQLEGLVVGEGIAMAHLKGAIYELAQALFGPDSKVRFQPVYFPFVEPGAQFAVWWPEGGKWLELGGAGMVHPKVFQAVDAYRERLGLPPAYRGVTGFAFGLGVERLAMLRYGIPDIRYFFGGRLKFLEQFKGVL 350
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344      

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

    Alignment length:785
                                    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       780     
           SYFB_THETH     1 MRVPFSWLKAYVPELESPEVLEERLAGLGFETDRIERVFPIPRGVVFARVLEAHPIPGTRLKRLVLDAGRTVEVVSGAENARKGIGVALALPGTELPGLGQKVGERVIQGVRSFGMALSPRELGVGEYGGGLLEFPEDALPPGTPLSEAWPEEVVLDLEVTPNRPDALGLLGLARDLHALGYALVEPEAALKAEALPLPFALKVEDPEGAPHFTLGYAFGLRVAPSPLWMQRALFAAGMRPINNVVDVTNYVMLERAQPMHAFDLRFVGEGIAVRRAREGERLKTLDGVERTLHPEDLVIAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHRFERGVDPLGQVPAQRRALSLLQALAGARVAEALLEAGSPKPPEAIPFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVTPPSHRLDLRLEEDLVEEVARIQGYETIPLALPAFFPAPDNRGVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDARRFRLDPPRLLLLNPLAPEKAALRTHLFPGLVRVLKENLDLDRPERALLFEVGRVFREREETHLAGLLFGEGVGLPWAKERLSGYFLLKGYLEALFARLGLAFRVEAQAFPFLHPGVSGRVLVEGEEVGFLGALHPEIAQELELPPVHLFELRLPLPDKPLAFQDPSRHPAAFRDLAVVVPAPTPYGEVEALVREAAGPYLESLALFDLYQGPPLPEGHKSLAFHLRFRHPKRTLRDEEVEEAVSRVAEALRARGFGLRGLDTP 785
               SCOP domains d2akwb1 B:1-38,B:152-190              d2akwb3 B:39-151 Domain B2 of PheRS-beta, PheT                                                                   d2akwb1 B:1-38,B:152-190               d2akwb4 B:191-399 B3/B4 domain of PheRS, PheT                                                                                                                                                                    d2akwb2 B:400-474 Domains B1 and B5 of PheRS-beta, PheT                    d2akwb6 B:475-681 Phenyl-tRNA synthetase (PheRS) beta subunit, PheT, central domain                                                                                                                            d2akwb5 B:682-785 Phenylalanyl-tRNA synthetase                                                           SCOP domains
               CATH domains 2akwB01 B:1-37,B:154-186             2akwB02 B:38-153 Nucleic acid-binding proteins                                                                      2akwB01 B:1-37,B:154-186         2akwB03 B:187-400 Phenylalanyl-trna Synthetase, Chain B, domain 3                                                                                                                                                     2akwB04 B:401-474  [code=3.30.56.20, no name defined]                     --------------2akwB05 B:489-679 Bira Bifunctional Protein; Domain 2                                                                                                                                          ----------2akwB06 B:690-775  [code=3.30.70.380, no name defined]                                ---------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhh.......hhhhhhhhhhhhh..eeeeee.......eeeeeeeeeee......eeeeee...eeeeee........eeeeee..............eeee..eeee.ee.hhhhhh..........ee........hhhhhh...eeeee.....hhhhhhhhhhhhhhhhh............ee......eeee.......eeeeeeee.......hhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeehhhhh.eeeeee.....eee.....eee.....eeeeeee..eeeeeee...ee............eeeeeee.hhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhh.eee...eee........eeehhhhhhhhhh...hhhhhhhhhhhh..eee.....eeee.........hhhhhhhhhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhh.ee.....ee..hhhhhh.......ee....hhhhhee...hhhhhhhhhhhhhhhh......eeeeeeee...eeeeeeeee....ee......ee.hhhhhhhhhhhhhhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhh.....eeeeee..................eeeeeeeeee...hhhhhhhhhhhhh...eeeeeeeeee........eeeeeeeeee.......hhhhhhhhhhhhhhhhhh......eeee. 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:688-780 UniProt: 688-780                                                     ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2akw B   1 MRVPFSWLKAYVPELESPEVLEERLAGLGFETDRIERVFPIPRGVVFARVLEAHPIPGTRLKRLVLDAGRTVEVVSGAENARKGIGVALALPGTELPGLGQKVGERVIQGVRSFGMALSPRELGVGEYGGGLLEFPEDALPPGTPLSEAWPEEVVLDLEVTPNRPDALGLLGLARDLHALGYALVEPEAALKAEALPLPFALKVEDPEGAPHFTLGYAFGLRVAPSPLWMQRALFAAGMRPINNVVDVTNYVMLERAQPMHAFDLRFVGEGIAVRRAREGERLKTLDGVERTLHPEDLVIAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHRFERGVDPLGQVPAQRRALSLLQALAGARVAEALLEAGSPKPPEAIPFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVTPPSHRLDLRLEEDLVEEVARIQGYETIPLALPAFFPAPDNRGVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDARRFRLDPPRLLLLNPLAPEKAALRTHLFPGLVRVLKENLDLDRPERALLFEVGRVFREREETHLAGLLFGEGVGLPWAKERLSGYFLLKGYLEALFARLGLAFRVEAQAFPFLHPGVSGRVLVEGEEVGFLGALHPEIAQELELPPVHLFELRLPLPDKPLAFQDPSRHPAAFRDLAVVVPAPTPYGEVEALVREAAGPYLESLALFDLYQGPPLPEGHKSLAFHLRFRHPKRTLRDEEVEEAVSRVAEALRARGFGLRGLDTP 785
                                    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       780     

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (6, 7)

Asymmetric Unit

(-) CATH Domains  (6, 7)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 27)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SYFA_THETH | P270011b70 1b7y 1eiy 2aly 2amc 2iy5 3hfz 3teh 4tva
        SYFB_THETH | P270021b70 1b7y 2aly 2amc 2iy5 3hfz 3teh 4tva

(-) Related Entries Specified in the PDB File

1b70 THE SAME PROTEIN COMPLEXED WITH PHE
1b7y THE SAME PROTEIN COMPLEXED WITH PHE-ADENYLATE ANALOGUE
1eiy THE SAME PROTEIN COMPLEXED WITH TRNA
1jjc THE SAME PROTEIN COMPLEXED WITH PHENYLALANYL-ADENYLATE
1pys NATIVE PROTEIN
2aly