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(-) Description

Title :  CRYSTAL STRUCTURE OF A LYSINE BIOSYNTHESIS ENZYME, LYSX, FROM THERMUS THERMOPHILUS HB8
 
Authors :  H. Sakai, M. N. Vassylyeva, T. Matsuura, S. Sekine, M. Nishiyama, T. Terada, M. Shirouzu, S. Kuramitsu, D. G. Vassylyev, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 Apr 03  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lysine Biosynthesis, Alpha-Aminoadipate Pathway, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Sakai, M. N. Vassylyeva, T. Matsuura, S. Sekine, K. Gotoh, M. Nishiyama, T. Terada, M. Shirouzu, S. Kuramitsu, D. G. Vassylyev, S. Yokoyama
Crystal Structure Of A Lysine Biosynthesis Enzyme, Lysx, From Thermus Thermophilus Hb8
J. Mol. Biol. V. 332 729 2003
PubMed-ID: 12963379  |  Reference-DOI: 10.1016/S0022-2836(03)00946-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSINE BIOSYNTHESIS ENZYME
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: LYSX

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 32)

Asymmetric/Biological Unit (2, 32)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2UNK30Mod. Amino Acid

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:129 , GLN A:169 , GLU A:170 , TYR A:171 , VAL A:172 , LYS A:174 , ASP A:178 , ARG A:194 , ASP A:237 , PHE A:239 , ASN A:248BINDING SITE FOR RESIDUE ADP A 300
2AC2SOFTWARELYS B:129 , GLN B:169 , GLU B:170 , VAL B:172 , LYS B:174 , ASP B:178 , ARG B:194 , ASP B:237 , PHE B:239 , ASN B:248 , GLU B:249BINDING SITE FOR RESIDUE ADP B 1300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UC9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:124 -Pro A:125
2Tyr B:124 -Pro B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UC9)

(-) Exons   (0, 0)

(no "Exon" information available for 1UC9)

(-) Sequences/Alignments

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:256
 aligned with LYSX_THET8 | Q5SH23 from UniProtKB/Swiss-Prot  Length:280

    Alignment length: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 280
               SCOP domains d1uc9a1 A:1-88 Lysine biosynthesis enzyme LysX, N-terminal domain                       d1uc9a2 A:89-280 Lysine biosynthesis enzyme L     ysX ATP-binding      domain                                                                                                                    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....-----................-----......eeeee........eeeeee..eeeeeee.--------------......hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee......hhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uc9 A   1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPKELEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIG-----xxxxxxxxxxxxxxxx-----GFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYR--------------AENCPLTEEVARLSVKAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILKYAWSLAS 280
                                    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
                                                                                                                                                              133     ||||||147-UNK|||   160                               194            209                                                                       
                                                                                                                                                                    139-UNK||148-UNK||                                                                                                                              
                                                                                                                                                                     140-UNK||149-UNK|                                                                                                                              
                                                                                                                                                                      141-UNK| 150-UNK                                                                                                                              
                                                                                                                                                                       142-UNK  151-UNK                                                                                                                             
                                                                                                                                                                        143-UNK  152-UNK                                                                                                                            
                                                                                                                                                                         144-UNK  153-UNK                                                                                                                           
                                                                                                                                                                          145-UNK  154-UNK                                                                                                                          
                                                                                                                                                                           146-UNK                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:253
 aligned with LYSX_THET8 | Q5SH23 from UniProtKB/Swiss-Prot  Length:280

    Alignment length: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 280
               SCOP domains d1uc9b1 B:1-88 Lysine biosynthesis enzyme LysX, N-terminal domain                       d1uc9b2 B:89-280 Lysine biosynthesis enzyme       LysX ATP-bindi       ng domain                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------RimK-1uc9B01 B:86-275                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------RimK-1uc9B02 B:86-275                                                                                                                                                                         ----- Pfam domains (2)
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh..eeeee.hhh.ee....hhhhh...eeee...hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeee...------..............-------......eeeee........eeeeee..eeeeeee.--------------......hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee......hhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uc9 B   1 MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPKELEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVI------xxxxxxxxxxxxxx-------GFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYR--------------AENCPLTEEVARLSVKAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILKYAWSLAS 280
                                    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
                                                                                                                                                             132      ||||||147-UNK|     160                               194            209                                                                       
                                                                                                                                                                    139-UNK||148-UNK                                                                                                                                
                                                                                                                                                                     140-UNK||149-UNK                                                                                                                               
                                                                                                                                                                      141-UNK| 150-UNK                                                                                                                              
                                                                                                                                                                       142-UNK  151-UNK                                                                                                                             
                                                                                                                                                                        143-UNK  152-UNK                                                                                                                            
                                                                                                                                                                         144-UNK                                                                                                                                    
                                                                                                                                                                          145-UNK                                                                                                                                   
                                                                                                                                                                           146-UNK
   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/Biological 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 1UC9)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: ATP-grasp (83)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LYSX_THET8 | Q5SH23: 1uc8 3vpd

(-) Related Entries Specified in the PDB File

1uc8 THE SAME PROTEIN, NO COMPLEX RELATED ID: TTK003000837.2 RELATED DB: TARGETDB