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(-) Description

Title :  CRYSTAL STRUCTURE OF L-ALLO-THREONINE ALDOLASE (TM1744) FROM THERMOTOGA MARITIMA AT 2.25 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  06 Jan 06  (Deposition) - 31 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tm1744, L-Allo-Threonine Aldolase, Structural Genomics, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Jcsg, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of L-Allo-Threonine Aldolase (Tm1744) Fro Thermotoga Maritima At 2. 25 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-ALLO-THREONINE ALDOLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: HK100
    Expression System Taxid: 562
    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  (5, 18)

Asymmetric/Biological Unit (5, 18)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL10Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
5NA1Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:288 , SER A:343 , HOH A:510 , ASN D:326 , GLU D:329 , HOH D:379BINDING SITE FOR RESIDUE CA A 344
02AC2SOFTWAREASP A:322 , HOH A:459 , ASN C:326 , GLU C:329 , HOH C:453 , HOH C:477 , HOH C:531BINDING SITE FOR RESIDUE CA A 345
03AC3SOFTWARETHR D:286 , LEU D:289 , VAL D:291 , HOH D:417 , HOH D:461 , HOH D:563BINDING SITE FOR RESIDUE NA D 344
04AC4SOFTWAREVAL B:25 , LYS C:11 , ARG C:17BINDING SITE FOR RESIDUE CL B 344
05AC5SOFTWAREGLN A:71 , ARG A:72 , HOH A:462 , GLN C:71 , ARG C:72 , HOH C:535BINDING SITE FOR RESIDUE CL A 346
06AC6SOFTWAREGLU A:24 , VAL A:25 , LYS D:11 , ARG D:17BINDING SITE FOR RESIDUE CL A 347
07AC7SOFTWAREGLN B:71 , ARG B:72 , HOH B:502 , HOH B:573 , GLN D:71 , ARG D:72BINDING SITE FOR RESIDUE CL D 345
08AC8SOFTWAREARG B:144 , VAL B:145 , LYS B:278 , HOH B:391BINDING SITE FOR RESIDUE CL B 345
09AC9SOFTWARELYS B:11 , ARG B:17 , VAL C:25BINDING SITE FOR RESIDUE CL B 346
10BC1SOFTWARELYS A:11 , ARG A:17 , VAL D:25BINDING SITE FOR RESIDUE CL A 348
11BC2SOFTWARELYS A:221 , ILE C:124BINDING SITE FOR RESIDUE CL C 344
12BC3SOFTWAREARG C:144 , VAL C:145 , LYS C:278 , HOH C:546BINDING SITE FOR RESIDUE CL C 345
13BC4SOFTWAREARG D:144 , VAL D:145 , LYS D:278 , HOH D:423 , HOH D:456BINDING SITE FOR RESIDUE CL D 346
14BC5SOFTWARELYS C:49 , GLY C:188 , ALA C:190 , ASP C:191 , HOH C:616BINDING SITE FOR RESIDUE GOL C 346

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FM1)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asn A:136 -Thr A:137
2Asn B:136 -Thr B:137
3Asn C:136 -Thr C:137
4His D:-1 -His D:0
5Asn D:136 -Thr D:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FM1)

(-) Exons   (0, 0)

(no "Exon" information available for 2FM1)

(-) 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 d2fm1a_ A: Low-specificity threonine aldolase                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2fm1A01 A:1-246 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   2fm1A02 A:247-342 Aspartate Aminotransferase, domain 1                                          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhh..hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee..hhhhhh..hhhhhhhh.eeeee.ee..eehhhhhhhhh.........eeeeeee...........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh.hhhhhhh...eeeee..........eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh...eeeee......hhhhhhhhhhhh.ee.eeee..eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fm1 A   1 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSkGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 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   
                                                                                                                                                                                                                                199-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 d2fm1b_ B: Low-specificity threonine aldolase                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2fm1B01 B:1-246 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   2fm1B02 B:247-342 Aspartate Aminotransferase, domain 1                                          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhh..hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee..hhhhhh..hhhhhhhh.eeeee.......hhhhhhhhh.........eeeeeee...........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh.hhhhhhh...eeeee..........eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh...eeeee......hhhhhhhhhhhh.ee.ee....eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fm1 B   1 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSkGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 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   
                                                                                                                                                                                                                                199-LLP                                                                                                                                            


Chain C 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 d2fm1c_ C: Low-specificity threonine aldolase                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2fm1C01 C:1-246 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   2fm1C02 C:247-342 Aspartate Aminotransferase, domain 1                                          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.........hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee..hhhhhh..hhhhhhhh.eeeee.......hhhhhhhhh.........eeeeeee...........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhh.hhhhhhhh..eeeee..........eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.ee.hhhh...eeeee......hhhhhhhhhhhh.ee.ee....eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fm1 C   1 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSkGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 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   
                                                                                                                                                                                                                                199-LLP                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:345
 aligned with Q9X266_THEMA | Q9X266 from UniProtKB/TrEMBL  Length:343

    Alignment length:345
                              1                                                                                                                                                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338     
         Q9X266_THEMA     - --MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 343
               SCOP domains d2fm1d_ D: Low-specificity threonine aldolase                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2fm1D01 D:-1-246 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                    2fm1D02 D:247-342 Aspartate Aminotransferase, domain 1                                          - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhhh..hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh....eeeee..hhhhhh..hhhhhhhh.eeeee.......hhhhhhhhh.........eeeeeee...........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh.hhhhhhh...eeeee..........eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh...eeeee......hhhhhhhhhhhh.ee.ee....eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fm1 D  -1 HHMIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMGNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGVPVKEYAGYADSVMFCLSkGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 343
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198|      208       218       228       238       248       258       268       278       288       298       308       318       328       338     
                                                                                                                                                                                                                                  199-LLP
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "Pfam Domain" information available for 2FM1)

(-) 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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 Related Entries

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UniProtKB/TrEMBL
        Q9X266_THEMA | Q9X266: 1jg8 1lw4 1lw5 1m6s

(-) Related Entries Specified in the PDB File

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