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(-) Description

Title :  LYSX FROM THERMUS THERMOPHILUS COMPLEXED WITH AMP-PNP
 
Authors :  T. Tomita, T. Ouchi, T. Kuzuyama, M. Nishiyama
Date :  29 Feb 12  (Deposition) - 27 Feb 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Atp-Dependenet Amine/Thiol Ligase Family, Atp-Dependenet Amine/Thiol Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ouchi, T. Tomita, A. Horie, A. Yoshida, K. Takahashi, H. Nishida, K. Lassak, H. Taka, R. Mineki, T. Fujimura, S. Kosono, C. Nishiyama, R. Masui, S. Kuramitsu, S. V. Albers, T. Kuzuyama, M. Nishiyama
Lysine And Arginine Biosyntheses Mediated By A Common Carrier Protein In Sulfolobus.
Nat. Chem. Biol. V. 9 277 2013
PubMed-ID: 23434852  |  Reference-DOI: 10.1038/NCHEMBIO.1200

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN S6 MODIFICATION PROTEIN
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-TTLYSX
    Expression System Strain: BL21CODONPLUS(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LYSX, RIMK
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: TTLYSX, RIMK

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2BUA2Ligand/IonBUTANOIC ACID
3CIT1Ligand/IonCITRIC ACID
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1ANP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2BUA4Ligand/IonBUTANOIC ACID
3CIT2Ligand/IonCITRIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:127 , LYS A:129 , TRP A:135 , GLY A:136 , LEU A:139 , GLN A:169 , GLU A:170 , VAL A:172 , LYS A:174 , ASP A:178 , ARG A:180 , ARG A:194 , TRP A:199 , ILE A:200 , THR A:201 , ASP A:237 , PHE A:239 , ASN A:248 , GLU A:249 , ASN A:251BINDING SITE FOR RESIDUE ANP A 301
2AC2SOFTWARETHR A:203 , PHE A:256 , LYS A:257 , ASN A:258 , SER A:259 , HOH A:608BINDING SITE FOR RESIDUE BUA A 302
3AC3SOFTWAREVAL A:57 , SER A:58 , GLN A:59 , SER A:60 , GLY A:133 , TRP A:135 , HOH A:585 , HOH A:597 , PHE B:161BINDING SITE FOR RESIDUE CIT A 303
4AC4SOFTWAREVAL B:127 , LYS B:129 , GLN B:169 , GLU B:170 , TYR B:171 , VAL B:172 , LYS B:174 , ASP B:178 , ARG B:180 , ARG B:194 , PHE B:239 , ASN B:248 , GLU B:249 , HOH B:426 , HOH B:496 , HOH B:532 , HOH B:575BINDING SITE FOR RESIDUE ANP B 301
5AC5SOFTWAREGLU B:255 , PHE B:256 , LYS B:257 , ASN B:258 , SER B:259BINDING SITE FOR RESIDUE BUA B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VPD)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Val A:77 -Asn A:78
2Tyr A:124 -Pro A:125
3Val B:77 -Asn B:78
4Tyr B:124 -Pro B:125
5Ser B:134 -Trp B:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VPD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VPD)

(-) Exons   (0, 0)

(no "Exon" information available for 3VPD)

(-) 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:281
 aligned with LYSX_THET8 | Q5SH23 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:281
                                                                                                                                                                                                                                                                                                                 280 
                                    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 
           LYSX_THET8     1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPKELEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLLAKVTDRAAAEALLEHKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYRRSAHWITNTARGGQAENCPLTEEVARLSVKAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILKYAWSLAS-   -
               SCOP domains d3vpda1 A:1-88 automated matches                                                        d3vpda2 A:89-281 automated matches                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh...eeeee.hhh.ee....hhhhh...eeee...hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhh..eeee..........eee.hhhhhhhhhhhhhhhhhhhhhheeeee......eeeeeeee..eeeeeeeee......hhhhh.eeee...hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee......hhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpd A   1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPEALEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLLAKVTDRAAAEALLEHKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYRRSAHWITNTARGGQAENCPLTEEIARLSVGAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILRYAWEVARG 281
                                    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 


Chain A from PDB  Type:PROTEIN  Length:281
 aligned with O50144_THETH | O50144 from UniProtKB/TrEMBL  Length:281

    Alignment length:281
                                    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 
         O50144_THETH     1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPEALEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLLAKVTDRAAAEALLEHKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYRRSAHWITNTARGGQAENCPLTEEIARLSVGAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILRYAWEVARG 281
               SCOP domains d3vpda1 A:1-88 automated matches                                                        d3vpda2 A:89-281 automated matches                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh...eeeee.hhh.ee....hhhhh...eeee...hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhh..eeee..........eee.hhhhhhhhhhhhhhhhhhhhhheeeee......eeeeeeee..eeeeeeeee......hhhhh.eeee...hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee......hhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpd A   1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPEALEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLLAKVTDRAAAEALLEHKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYRRSAHWITNTARGGQAENCPLTEEIARLSVGAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILRYAWEVARG 281
                                    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 


Chain B from PDB  Type:PROTEIN  Length:268
 aligned with LYSX_THET8 | Q5SH23 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:281
                                                                                                                                                                                                                                                                                                                 280 
                                    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 
           LYSX_THET8     1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPKELEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLLAKVTDRAAAEALLEHKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYRRSAHWITNTARGGQAENCPLTEEVARLSVKAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILKYAWSLAS-   -
               SCOP domains d3vpdb1 B:1-88 automated matches                                                        d3vpdb2 B:89-281 automated matches                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh..eeeee.hhh.ee....hhhhh...eeee...hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeee..........eee.hhhhhhhhhhhhhhhhhhhhhheeeee.......eeeeeee..eeeeeeee-------------..ee...hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee....hhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpd B   1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPEALEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLLAKVTDRAAAEALLEHKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYR-------------QAENCPLTEEIARLSVGAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILRYAWEVARG 281
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   |     -       210       220       230       240       250       260       270       280 
                                                                                                                                                                                                                           194           208                                                                         


Chain B from PDB  Type:PROTEIN  Length:268
 aligned with O50144_THETH | O50144 from UniProtKB/TrEMBL  Length:281

    Alignment length:281
                                    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 
         O50144_THETH     1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPEALEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLLAKVTDRAAAEALLEHKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYRRSAHWITNTARGGQAENCPLTEEIARLSVGAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILRYAWEVARG 281
               SCOP domains d3vpdb1 B:1-88 automated matches                                                        d3vpdb2 B:89-281 automated matches                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh..eeeee.hhh.ee....hhhhh...eeee...hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeee..........eee.hhhhhhhhhhhhhhhhhhhhhheeeee.......eeeeeee..eeeeeeee-------------..ee...hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee....hhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpd B   1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPEALEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLLAKVTDRAAAEALLEHKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYR-------------QAENCPLTEEIARLSVGAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILRYAWEVARG 281
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   |     -       210       220       230       240       250       260       270       280 
                                                                                                                                                                                                                           194           208
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VPD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VPD)

(-) Gene Ontology  (9, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LYSX_THET8 | Q5SH23)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0019878    lysine biosynthetic process via aminoadipic acid    The chemical reactions and pathways resulting in the formation of lysine by the aminoadipic pathway.

Chain A,B   (O50144_THETH | O50144)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.

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  O50144_THETH | O50144
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 Related Entries

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

UniProtKB/Swiss-Prot
        LYSX_THET8 | Q5SH23: 1uc8 1uc9

(-) Related Entries Specified in the PDB File

3vpb 3vpc