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(-) Description

Title :  CRYSTAL STRUCTURE OF THREONINE ALDOLASE (LOW-SPECIFICITY)
 
Authors :  C. L. Kielkopf, J. Bonanno, S. Ray, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  23 Jun 01  (Deposition) - 04 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Glycine Biosynthesis, Threonine Aldolase, Pyridoxal-5'- Phosphate, Calcium Binding Site, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Kielkopf, J. Bonanno, S. Ray, S. K. Burley
Crystal Structure Of Low-Specificity Threonine Aldolase, A Key Enzyme In Glycine Biosynthesis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-ALLO-THREONINE ALDOLASE
    Chains: A, B, C, D
    EC Number: 4.1.2.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSKB2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TM1744
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:12 , THR B:14 , SER B:202 , ALA B:207 , GLN C:236BINDING SITE FOR RESIDUE CA B 901
2AC2SOFTWARETHR A:12 , THR A:14 , SER A:202 , ALA A:207 , GLN D:236BINDING SITE FOR RESIDUE CA A 902
3AC3SOFTWAREGLN A:236 , THR D:12 , THR D:14 , SER D:202 , ALA D:207BINDING SITE FOR RESIDUE CA D 903
4AC4SOFTWAREGLN B:236 , THR C:12 , THR C:14 , SER C:202 , ALA C:207BINDING SITE FOR RESIDUE CA C 904
5AC5SOFTWAREASP A:326 , ASN B:330 , GLU B:333 , HOH B:992BINDING SITE FOR RESIDUE CA B 905
6AC6SOFTWAREASN A:292 , SER A:347 , HOH A:936 , ASN D:330 , GLU D:333 , HOH D:970BINDING SITE FOR RESIDUE CA D 906
7AC7SOFTWAREGLN A:75 , ARG A:76 , HOH A:1005 , GLN B:75 , ARG B:76 , HOH B:1045BINDING SITE FOR RESIDUE NA A 907
8AC8SOFTWAREGLN C:75 , ARG C:76 , HOH C:981 , GLN D:75 , ARG D:76BINDING SITE FOR RESIDUE NA C 908

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JG8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JG8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JG8)

(-) Exons   (0, 0)

(no "Exon" information available for 1JG8)

(-) 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:343
 aligned with Q9X266_THEMA | Q9X266 from UniProtKB/TrEMBL  Length:343

    Alignment length:343
                                    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   
         Q9X266_THEMA     1 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 343
               SCOP domains d1jg8a_ A: Low-specificity threonine aldolase                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1jg8A01 A:5-250 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   1jg8A02 A:251-346 Aspartate Aminotransferase, domain 1                                          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhh..hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee..hhhhhh..hhhhhhh..eeeee.ee..eehhhhhhhhh.........eeeeeee...........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhh.hhhhhhhh..eeeee..........eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh...eeeee......hhhhhhhhhhhhhee.eeee..eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jg8 A   5 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSkGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 347
                                    14        24        34        44        54        64        74        84        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   
                                                                                                                                                                                                                                203-LLP                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:343
 aligned with Q9X266_THEMA | Q9X266 from UniProtKB/TrEMBL  Length:343

    Alignment length:343
                                    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   
         Q9X266_THEMA     1 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 343
               SCOP domains d1jg8b_ B: Low-specificity threonine aldolase                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1jg8B01 B:5-250 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   1jg8B02 B:251-346 Aspartate Aminotransferase, domain 1                                          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhh..hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh....eeeee..hhhhhh..hhhhhhhh.eeeee.ee..eehhhhhhhhh.........eeeeeee...........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhh.hhhhhhhh..eeeee..........eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh...eeeee......hhhhhhhhhhhh.ee.ee....eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jg8 B   5 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSkGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 347
                                    14        24        34        44        54        64        74        84        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   
                                                                                                                                                                                                                                203-LLP                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:340
 aligned with Q9X266_THEMA | Q9X266 from UniProtKB/TrEMBL  Length:343

    Alignment length:343
                                    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   
         Q9X266_THEMA     1 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 343
               SCOP domains d1jg8c_ C: Low-speci   ficity threonine aldolase                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1jg8C01 C:5-250 Type    I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                1jg8C02 C:251-345 Aspartate Aminotransferase, domain 1                                         -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhh..hhhhhhhh---...hhhhh.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee..hhhhhh..hhhhhhhh.eeeee.ee..eehhhhhhhhh.........eeeeeee...........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhh.hhhhhhh...eeeee..........eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh...eeeee......hhhhhhhhhhhh.ee.ee....eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jg8 C   5 MIDLRSDTVTKPTEEMRKAM---EVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSkGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 347
                                    14        24   |    34        44        54        64        74        84        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   
                                              24  28                                                                                                                                                                            203-LLP                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:344
 aligned with Q9X266_THEMA | Q9X266 from UniProtKB/TrEMBL  Length:343

    Alignment length:344
                             1                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339    
         Q9X266_THEMA     - -MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 343
               SCOP domains d1jg8d_ D: Low-specificity threonine aldolase                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -1jg8D01 D:5-250 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   1jg8D02 D:251-346 Aspartate Aminotransferase, domain 1                                          - CATH domains
           Pfam domains (1) ---Beta_elim_lyase-1jg8D01 D:7-292                                                                                                                                                                                                                                                               ------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---Beta_elim_lyase-1jg8D02 D:7-292                                                                                                                                                                                                                                                               ------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---Beta_elim_lyase-1jg8D03 D:7-292                                                                                                                                                                                                                                                               ------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---Beta_elim_lyase-1jg8D04 D:7-292                                                                                                                                                                                                                                                               ------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..ee..hhhhh..hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh....eeeee..hhhhhh..hhhhhhhh.eeeee.......hhhhhhhhh.........eeeeeee...........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhh.hhhhhhh...eeeee..........eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh...eeeee......hhhhhhhhhhhh.ee.ee....eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jg8 D   4 MMIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSkGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 347
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343    
                                                                                                                                                                                                                                 203-LLP
   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  (1, 4)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9X266_THEMA | Q9X266)
molecular function
    GO:0008732    L-allo-threonine aldolase activity    Catalysis of the reaction: L-allo-threonine = glycine + acetaldehyde.
    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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004793    threonine aldolase activity    Catalysis of the reaction: L-threonine = glycine + acetaldehyde.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0006567    threonine catabolic process    The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1jg8
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  Q9X266_THEMA | Q9X266
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 Related Entries

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UniProtKB/TrEMBL
        Q9X266_THEMA | Q9X266: 1lw4 1lw5 1m6s 2fm1

(-) Related Entries Specified in the PDB File

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