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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE 4-AMINO-4-DEOXYCHORISMATE LYASE
 
Authors :  B. Padmanabhan, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 Jan 08  (Deposition) - 22 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ttha0621, Plp Cofactor, Pyridoxal Enzyme, Lyase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Padmanabhan, Y. Bessho, A. Ebihara, S. V. Antonyuk, M. J. Ellis, R. W. Strange, S. Kuramitsu, N. Watanabe, S. S. Hasnain, S. Yokoyama
Structure Of Putative 4-Amino-4-Deoxychorismate Lyase From Thermus Thermophilus Hb8.
Acta Crystallogr. , Sect. F V. 65 1234 2009
PubMed-ID: 20054118  |  Reference-DOI: 10.1107/S1744309109050052

(-) Compounds

Molecule 1 - PUTATIVE 4-AMINO-4-DEOXYCHORISMATE LYASE
    Chains: A, B, C, D
    EC Number: 4.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11-A
    Expression System Strain: B834(DE3)
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Strain: HB8

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE2Ligand/IonTRIETHYLENE GLYCOL
4PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
5SO44Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:47 , HIS A:48 , ARG A:124BINDING SITE FOR RESIDUE SO4 A 247
02AC2SOFTWAREARG B:44 , ARG B:47 , HIS B:48BINDING SITE FOR RESIDUE SO4 B 247
03AC3SOFTWAREARG C:44 , ARG C:47 , HIS C:48BINDING SITE FOR RESIDUE SO4 C 247
04AC4SOFTWAREARG D:44 , ARG D:47 , HIS D:48 , GLU D:181BINDING SITE FOR RESIDUE SO4 D 247
05AC5SOFTWAREARG A:44 , LYS A:126 , TYR A:133 , ASP A:159 , GLY A:160 , SER A:161 , ARG A:162 , THR A:163 , SER A:164 , LEU A:180 , GLY A:182 , ILE A:183 , THR A:184 , GLY A:217 , SER A:218BINDING SITE FOR RESIDUE PLP A 248
06AC6SOFTWAREARG B:44 , LYS B:126 , TYR B:133 , ASP B:159 , GLY B:160 , SER B:161 , ARG B:162 , THR B:163 , SER B:164 , LEU B:180 , GLY B:182 , ILE B:183 , THR B:184 , GLY B:217 , SER B:218BINDING SITE FOR RESIDUE PLP B 248
07AC7SOFTWAREARG C:44 , LYS C:126 , TYR C:133 , ASP C:159 , GLY C:160 , SER C:161 , ARG C:162 , THR C:163 , SER C:164 , LEU C:180 , GLY C:182 , ILE C:183 , THR C:184 , GLY C:217 , SER C:218BINDING SITE FOR RESIDUE PLP C 248
08AC8SOFTWAREARG D:44 , LYS D:126 , TYR D:133 , ASP D:159 , GLY D:160 , SER D:161 , ARG D:162 , THR D:163 , SER D:164 , LEU D:180 , GLY D:182 , ILE D:183 , THR D:184 , GLY D:217 , SER D:218BINDING SITE FOR RESIDUE PLP D 248
09AC9SOFTWAREARG C:46 , TYR C:56 , GLY C:58 , ASP C:59 , GLU C:60BINDING SITE FOR RESIDUE PGE C 249
10BC1SOFTWARELEU A:203 , PHE A:204 , ARG A:205BINDING SITE FOR RESIDUE PGE A 249
11BC2SOFTWAREPHE B:204BINDING SITE FOR RESIDUE PEG B 249
12BC3SOFTWARELEU B:240 , PRO D:99 , PRO D:101BINDING SITE FOR RESIDUE PEG D 249
13BC4SOFTWAREARG B:201 , ARG D:169 , ARG D:210BINDING SITE FOR RESIDUE PEG B 250

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:78 -A:243
2B:78 -B:243
3C:78 -C:243
4D:78 -D:243

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZGI)

(-) 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:244
 aligned with Q5SKM2_THET8 | Q5SKM2 from UniProtKB/TrEMBL  Length:246

    Alignment length:244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
         Q5SKM2_THET8     1 MRLLNGTPLALALPEAFLYHGASVFTTLRAEGGRPLWLEEHLARLRRHALALGLSYPGDEAFLEDLEALLRAFPKAPCLRLRFTVGEGVRLSEARPYAPLPLSLYREGVRVRLTGYRVHPDLARYKTGNYLPYRLALEEARKEGAFEGLLLDAFGHVVDGSRTSPLLFREGTLYLLEGGLEGITREKVAEAARGLGLRVERGLFRPEGLRGHLLLAGSGVGLLPVRPPPPELLPLIERFLPACY 244
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..ee.....hhhhhhh...eeeeeeee..ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......eeeeeeeee..eeeeeeee.....hhhhhhh..eeeeeee............hhhhhhhhhhhhh....eeeee.....eeee...eeeeee..eeeee.....hhhhhhhhhhhhhh..eeeee..hhhhh..eeeeee...eeee....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zgi A   1 mRLLNGTPLALALPEAFLYHGASVFTTLRAEGGRPLWLEEHLARLRRHALALGLSYPGDEAFLEDLEALLRAFPKAPCLRLRFTVGEGVRLSEARPYAPLPLSLYREGVRVRLTGYRVHPDLARYKTGNYLPYRLALEEARKEGAFEGLLLDAFGHVVDGSRTSPLLFREGTLYLLEGGLEGITREKVAEAARGLGLRVERGLFRPEGLRGHLLLAGSGVGLLPVRPPPPELLPLIERFLPACY 244
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
                            |                                                                                                                                                                                                                                                   
                            1-MSE                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q5SKM2_THET8 | Q5SKM2 from UniProtKB/TrEMBL  Length:246

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
         Q5SKM2_THET8     1 MRLLNGTPLALALPEAFLYHGASVFTTLRAEGGRPLWLEEHLARLRRHALALGLSYPGDEAFLEDLEALLRAFPKAPCLRLRFTVGEGVRLSEARPYAPLPLSLYREGVRVRLTGYRVHPDLARYKTGNYLPYRLALEEARKEGAFEGLLLDAFGHVVDGSRTSPLLFREGTLYLLEGGLEGITREKVAEAARGLGLRVERGLFRPEGLRGHLLLAGSGVGLLPVRPPPPELLPLIERFLPACYT 245
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee....hhhhhhhh..eeeeeeee..ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......eeeeeeee..eeeeeeee......hhhhhh..eeeeeee............hhhhhhhhhhhhhh...eeeee.....eeee...eeeeee..eeeee.....hhhhhhhhhhhhhh..eeeee..hhhhh..eeeeee...eeee....hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zgi B   1 mRLLNGTPLALALPEAFLYHGASVFTTLRAEGGRPLWLEEHLARLRRHALALGLSYPGDEAFLEDLEALLRAFPKAPCLRLRFTVGEGVRLSEARPYAPLPLSLYREGVRVRLTGYRVHPDLARYKTGNYLPYRLALEEARKEGAFEGLLLDAFGHVVDGSRTSPLLFREGTLYLLEGGLEGITREKVAEAARGLGLRVERGLFRPEGLRGHLLLAGSGVGLLPVRPPPPELLPLIERFLPACYT 245
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
                            1-MSE                                                                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:245
 aligned with Q5SKM2_THET8 | Q5SKM2 from UniProtKB/TrEMBL  Length:246

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
         Q5SKM2_THET8     1 MRLLNGTPLALALPEAFLYHGASVFTTLRAEGGRPLWLEEHLARLRRHALALGLSYPGDEAFLEDLEALLRAFPKAPCLRLRFTVGEGVRLSEARPYAPLPLSLYREGVRVRLTGYRVHPDLARYKTGNYLPYRLALEEARKEGAFEGLLLDAFGHVVDGSRTSPLLFREGTLYLLEGGLEGITREKVAEAARGLGLRVERGLFRPEGLRGHLLLAGSGVGLLPVRPPPPELLPLIERFLPACYT 245
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..ee.....hhhhhhh...eeeeeeee..ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee......hhhhhh..eeeeeee............hhhhhhhhhhhhhh...eeeee.....eeee...eeeeee..eeeee.....hhhhhhhhhhhhhh..eeeee..hhhhh..eeeeee...eeee....hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zgi C   1 mRLLNGTPLALALPEAFLYHGASVFTTLRAEGGRPLWLEEHLARLRRHALALGLSYPGDEAFLEDLEALLRAFPKAPCLRLRFTVGEGVRLSEARPYAPLPLSLYREGVRVRLTGYRVHPDLARYKTGNYLPYRLALEEARKEGAFEGLLLDAFGHVVDGSRTSPLLFREGTLYLLEGGLEGITREKVAEAARGLGLRVERGLFRPEGLRGHLLLAGSGVGLLPVRPPPPELLPLIERFLPACYT 245
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
                            1-MSE                                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:246
 aligned with Q5SKM2_THET8 | Q5SKM2 from UniProtKB/TrEMBL  Length:246

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
         Q5SKM2_THET8     1 MRLLNGTPLALALPEAFLYHGASVFTTLRAEGGRPLWLEEHLARLRRHALALGLSYPGDEAFLEDLEALLRAFPKAPCLRLRFTVGEGVRLSEARPYAPLPLSLYREGVRVRLTGYRVHPDLARYKTGNYLPYRLALEEARKEGAFEGLLLDAFGHVVDGSRTSPLLFREGTLYLLEGGLEGITREKVAEAARGLGLRVERGLFRPEGLRGHLLLAGSGVGLLPVRPPPPELLPLIERFLPACYTE 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------Aminotran_4-2zgiD01 D:36-231                                                                                                                                                                        --------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------Aminotran_4-2zgiD02 D:36-231                                                                                                                                                                        --------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------Aminotran_4-2zgiD03 D:36-231                                                                                                                                                                        --------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------Aminotran_4-2zgiD04 D:36-231                                                                                                                                                                        --------------- Pfam domains (4)
         Sec.struct. author .eee..ee.....hhhhhhh...eeeeeeee..ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee.....hhhhhhh..eeeeeee............hhhhhhhhhhhhhh...eeeee.....eeee...eeeeee..eeeee.....hhhhhhhhhhhhhh..eeeee..hhhhh..eeeeee...eeee.......hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zgi D   1 mRLLNGTPLALALPEAFLYHGASVFTTLRAEGGRPLWLEEHLARLRRHALALGLSYPGDEAFLEDLEALLRAFPKAPCLRLRFTVGEGVRLSEARPYAPLPLSLYREGVRVRLTGYRVHPDLARYKTGNYLPYRLALEEARKEGAFEGLLLDAFGHVVDGSRTSPLLFREGTLYLLEGGLEGITREKVAEAARGLGLRVERGLFRPEGLRGHLLLAGSGVGLLPVRPPPPELLPLIERFLPACYTE 246
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
                            1-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2ZGI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZGI)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Aminotran_4] (8)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SKM2_THET8 | Q5SKM2)
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: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.
biological process
    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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