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(-) Description

Title :  CRYSTAL STRUCTURE OF N-ACYLAMINO ACID RACEMASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Hayashida, S. H. Kim, K. Takeda, T. Hisano, K. Miki
Date :  05 Nov 07  (Deposition) - 26 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Octamer, Tim Beta/Alpha-Barrel, Metal-Binding, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hayashida, S. H. Kim, K. Takeda, T. Hisano, K. Miki
Crystal Structure Of N-Acylamino Acid Racemase From Thermus Thermophilus Hb8
Proteins V. 71 519 2008
PubMed-ID: 18214979  |  Reference-DOI: 10.1002/PROT.21926

(-) Compounds

Molecule 1 - N-ACYLAMINO ACID RACEMASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET11A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2ZC8)

(-) Sites  (0, 0)

(no "Site" information available for 2ZC8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZC8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZC8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZC8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZC8)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZC8)

(-) 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:368
 aligned with Q5SJX8_THET8 | Q5SJX8 from UniProtKB/TrEMBL  Length:369

    Alignment length:368
                                    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        
         Q5SJX8_THET8     1 MRIEAAELRILELPLKFRFETSFGVQTKRTILLLRLFGEGLEGLGEGVMERLPLYREETVAGARYLLEEVFLPRVLGRDLPNPEALREALAPFRGNPMAKAVLEMAFFDLWAKALGRPLWQVLGGVRQAVEVGVSLGIQPSVEDTLRVVERHLEEGYRRIKLKIKPGWDYEVLKAVREAFPEATLTADANSAYSLANLAQLKRLDELRLDYIEQPLAYDDLLDHAKLQRELSTPICLDESLTGAEKARKAIELGAGRVFNVKPARLGGHGESLRVHALAESAGIPLWMGGMLEAGVGRAHNLHLATLPGFTKPGDVSSASRYWEEDIVEEALEAKDGLMPVPEGVGIGVHLKLPFVERVTLWQRYMSA 368
               SCOP domains d2zc8a1 A:1-125 automated matches                                                                                            d2zc8a2 A:126-368 automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2zc8A02 A:117-346 Enolase superfamily                                                                                                                                                                                                 ---------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeee............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhh....eee..eee....hhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh............hhhhh...............eee...........hhhhhhhheeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc8 A   1 MRIEAAELRILELPLKFRFETSFGVQTKRTILLLRLFGEGLEGLGEGVMERLPLYREETVAGARYLLEEVFLPRVLGRDLPNPEALREALAPFRGNPMAKAVLEMAFFDLWAKALGRPLWQVLGGVRQAVEVGVSLGIQPSVEDTLRVVERHLEEGYRRIKLKIKPGWDYEVLKAVREAFPEATLTADANSAYSLANLAQLKRLDELRLDYIEQPLAYDDLLDHAKLQRELSTPICLDESLTGAEKARKAIELGAGRVFNVKPARLGGHGESLRVHALAESAGIPLWMGGMLEAGVGRAHNLHLATLPGFTKPGDVSSASRYWEEDIVEEALEAKDGLMPVPEGVGIGVHLKLPFVERVTLWQRYMSA 368
                                    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        


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with Q5SJX8_THET8 | Q5SJX8 from UniProtKB/TrEMBL  Length:369

    Alignment length:368
                                    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        
         Q5SJX8_THET8     1 MRIEAAELRILELPLKFRFETSFGVQTKRTILLLRLFGEGLEGLGEGVMERLPLYREETVAGARYLLEEVFLPRVLGRDLPNPEALREALAPFRGNPMAKAVLEMAFFDLWAKALGRPLWQVLGGVRQAVEVGVSLGIQPSVEDTLRVVERHLEEGYRRIKLKIKPGWDYEVLKAVREAFPEATLTADANSAYSLANLAQLKRLDELRLDYIEQPLAYDDLLDHAKLQRELSTPICLDESLTGAEKARKAIELGAGRVFNVKPARLGGHGESLRVHALAESAGIPLWMGGMLEAGVGRAHNLHLATLPGFTKPGDVSSASRYWEEDIVEEALEAKDGLMPVPEGVGIGVHLKLPFVERVTLWQRYMSA 368
               SCOP domains d2zc8b1 B:1-125 automated matches                                                                                            d2zc8b2 B:126-368 automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2zc8B02 B:117-346 Enolase superfamily                                                                                                                                                                                                 ---------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeee............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eee..eee....hhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh............hhhhh...............eee...........hhhhhhhheeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc8 B   1 MRIEAAELRILELPLKFRFETSFGVQTKRTILLLRLFGEGLEGLGEGVMERLPLYREETVAGARYLLEEVFLPRVLGRDLPNPEALREALAPFRGNPMAKAVLEMAFFDLWAKALGRPLWQVLGGVRQAVEVGVSLGIQPSVEDTLRVVERHLEEGYRRIKLKIKPGWDYEVLKAVREAFPEATLTADANSAYSLANLAQLKRLDELRLDYIEQPLAYDDLLDHAKLQRELSTPICLDESLTGAEKARKAIELGAGRVFNVKPARLGGHGESLRVHALAESAGIPLWMGGMLEAGVGRAHNLHLATLPGFTKPGDVSSASRYWEEDIVEEALEAKDGLMPVPEGVGIGVHLKLPFVERVTLWQRYMSA 368
                                    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
   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZC8)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SJX8_THET8 | Q5SJX8)
molecular function
    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:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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