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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HMG-COA LYASE FROM BRUCELLA MELITENSIS, NORTHEAST STRUCTURAL GENOMICS TARGET LR35.
 
Authors :  F. Forouhar, M. Abashidze, M. Hussain, S. M. Vorobiev, R. Xiao, M. Ciano T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structur Genomics Consortium (Nesg)
Date :  24 Dec 04  (Deposition) - 05 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Tim-Barrel Protein, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, M. Hussain, R. Farid, J. Benach, M. Abashidze, W. C. Edstrom, S. M. Vorobiev, R. Xiao, T. B. Acton, Z. Fu, J. J. Kim, H. M. Miziorko, G. T. Montelione, J. F. Hunt
Crystal Structures Of Two Bacterial 3-Hydroxy-3-Methylglutaryl-Coa Lyases Suggest A Common Catalytic Mechanism Among A Family Of Tim Barrel Metalloenzymes Cleaving Carbon-Carbon Bonds.
J. Biol. Chem. V. 281 7533 2006
PubMed-ID: 16330546  |  Reference-DOI: 10.1074/JBC.M507996200

(-) Compounds

Molecule 1 - HYDROXYMETHYLGLUTARYL-COA LYASE
    Chains: A, B, C, D
    EC Number: 4.1.3.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PET21
    Organism Scientific: BRUCELLA MELITENSIS
    Organism Taxid: 224914
    Strain: 16M

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:14 , HIS A:205 , HIS A:207 , ASN A:247BINDING SITE FOR RESIDUE CA A 601
2AC2SOFTWAREASP B:14 , HIS B:205 , HIS B:207 , ASN B:247 , HOH B:661 , HOH B:667BINDING SITE FOR RESIDUE CA B 602
3AC3SOFTWAREASP C:14 , HIS C:205 , HIS C:207 , ASN C:247BINDING SITE FOR RESIDUE CA C 603
4AC4SOFTWAREASP D:14 , HIS D:205 , HIS D:207 , ASN D:247BINDING SITE FOR RESIDUE CA D 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YDN)

(-) 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:283
 aligned with Q8YEF2_BRUME | Q8YEF2 from UniProtKB/TrEMBL  Length:287

    Alignment length:283
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281   
         Q8YEF2_BRUME     2 AEHVEIVEMAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADSREVMAGIRRADGVRYSVLVPNMKGYEAAAAAHADEIAVFISASEGFSKANINCTIAESIERLSPVIGAAINDGLAIRGYVSCVVECPYDGPVTPQAVASVTEQLFSLGCHEVSLGDTIGRGTPDTVAAMLDAVLAIAPAHSLAGHYHDTGGRALDNIRVSLEKGLRVFDASVGGLGGCPFAPGAKGNVDTVAVVEMLHEMGFETGLDLDRLRSAGLFTQALRQD 284
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhhh.....hhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhh...eeeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeee...ee...ee.hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..hhh.eeeee.....hhhhhhhhhhhhh..eeee..................hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydn A   2 AEHVEIVEmAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADSREVmAGIRRADGVRYSVLVPNmKGYEAAAAAHADEIAVFISASEGFSKANINCTIAESIERLSPVIGAAINDGLAIRGYVSCVVECPYDGPVTPQAVASVTEQLFSLGCHEVSLGDTIGRGTPDTVAAmLDAVLAIAPAHSLAGHYHDTGGRALDNIRVSLEKGLRVFDASVGGLGGCPFAPGAKGNVDTVAVVEmLHEmGFETGLDLDRLRSAGLFTQALRQD 284
                                    11        21        31        41        51        61  |     71        81|       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    |  261       271       281   
                                   10-MSE                                                64-MSE            82-MSE                                                                                                    189-MSE                                                            256-MSE                        
                                                                                                                                                                                                                                                                                            260-MSE                    


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with Q8YEF2_BRUME | Q8YEF2 from UniProtKB/TrEMBL  Length:287

    Alignment length:283
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281   
         Q8YEF2_BRUME     2 AEHVEIVEMAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADSREVMAGIRRADGVRYSVLVPNMKGYEAAAAAHADEIAVFISASEGFSKANINCTIAESIERLSPVIGAAINDGLAIRGYVSCVVECPYDGPVTPQAVASVTEQLFSLGCHEVSLGDTIGRGTPDTVAAMLDAVLAIAPAHSLAGHYHDTGGRALDNIRVSLEKGLRVFDASVGGLGGCPFAPGAKGNVDTVAVVEMLHEMGFETGLDLDRLRSAGLFTQALRQD 284
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhhh.....hhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhh...eeeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeee...ee...ee.hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..hhh.eeeee.....hhhhhhhhhhhhh..eeee..................hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydn B   2 AEHVEIVEmAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADSREVmAGIRRADGVRYSVLVPNmKGYEAAAAAHADEIAVFISASEGFSKANINCTIAESIERLSPVIGAAINDGLAIRGYVSCVVECPYDGPVTPQAVASVTEQLFSLGCHEVSLGDTIGRGTPDTVAAmLDAVLAIAPAHSLAGHYHDTGGRALDNIRVSLEKGLRVFDASVGGLGGCPFAPGAKGNVDTVAVVEmLHEmGFETGLDLDRLRSAGLFTQALRQD 284
                                    11        21        31        41        51        61  |     71        81|       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    |  261       271       281   
                                   10-MSE                                                64-MSE            82-MSE                                                                                                    189-MSE                                                            256-MSE                        
                                                                                                                                                                                                                                                                                            260-MSE                    


Chain C from PDB  Type:PROTEIN  Length:283
 aligned with Q8YEF2_BRUME | Q8YEF2 from UniProtKB/TrEMBL  Length:287

    Alignment length:283
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281   
         Q8YEF2_BRUME     2 AEHVEIVEMAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADSREVMAGIRRADGVRYSVLVPNMKGYEAAAAAHADEIAVFISASEGFSKANINCTIAESIERLSPVIGAAINDGLAIRGYVSCVVECPYDGPVTPQAVASVTEQLFSLGCHEVSLGDTIGRGTPDTVAAMLDAVLAIAPAHSLAGHYHDTGGRALDNIRVSLEKGLRVFDASVGGLGGCPFAPGAKGNVDTVAVVEMLHEMGFETGLDLDRLRSAGLFTQALRQD 284
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhhh.....hhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhh...eeeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeee...ee...ee.hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..hhh.eeeee.....hhhhhhhhhhhhh..eeee..................hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydn C   2 AEHVEIVEmAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADSREVmAGIRRADGVRYSVLVPNmKGYEAAAAAHADEIAVFISASEGFSKANINCTIAESIERLSPVIGAAINDGLAIRGYVSCVVECPYDGPVTPQAVASVTEQLFSLGCHEVSLGDTIGRGTPDTVAAmLDAVLAIAPAHSLAGHYHDTGGRALDNIRVSLEKGLRVFDASVGGLGGCPFAPGAKGNVDTVAVVEmLHEmGFETGLDLDRLRSAGLFTQALRQD 284
                                    11        21        31        41        51        61  |     71        81|       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    |  261       271       281   
                                   10-MSE                                                64-MSE            82-MSE                                                                                                    189-MSE                                                            256-MSE                        
                                                                                                                                                                                                                                                                                            260-MSE                    


Chain D from PDB  Type:PROTEIN  Length:283
 aligned with Q8YEF2_BRUME | Q8YEF2 from UniProtKB/TrEMBL  Length:287

    Alignment length:283
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281   
         Q8YEF2_BRUME     2 AEHVEIVEMAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADSREVMAGIRRADGVRYSVLVPNMKGYEAAAAAHADEIAVFISASEGFSKANINCTIAESIERLSPVIGAAINDGLAIRGYVSCVVECPYDGPVTPQAVASVTEQLFSLGCHEVSLGDTIGRGTPDTVAAMLDAVLAIAPAHSLAGHYHDTGGRALDNIRVSLEKGLRVFDASVGGLGGCPFAPGAKGNVDTVAVVEMLHEMGFETGLDLDRLRSAGLFTQALRQD 284
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------HMGL-like-1ydnD01 D:13-261                                                                                                                                                                                                                               ----------------------- Pfam domains (1)
           Pfam domains (2) -----------HMGL-like-1ydnD02 D:13-261                                                                                                                                                                                                                               ----------------------- Pfam domains (2)
           Pfam domains (3) -----------HMGL-like-1ydnD03 D:13-261                                                                                                                                                                                                                               ----------------------- Pfam domains (3)
           Pfam domains (4) -----------HMGL-like-1ydnD04 D:13-261                                                                                                                                                                                                                               ----------------------- Pfam domains (4)
         Sec.struct. author ....eeee...hhhhhh.....hhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhh...eeeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeee...ee...ee.hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..hhh.eeeee.....hhhhhhhhhhhhh..eeee..................hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydn D   2 AEHVEIVEmAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADSREVmAGIRRADGVRYSVLVPNmKGYEAAAAAHADEIAVFISASEGFSKANINCTIAESIERLSPVIGAAINDGLAIRGYVSCVVECPYDGPVTPQAVASVTEQLFSLGCHEVSLGDTIGRGTPDTVAAmLDAVLAIAPAHSLAGHYHDTGGRALDNIRVSLEKGLRVFDASVGGLGGCPFAPGAKGNVDTVAVVEmLHEmGFETGLDLDRLRSAGLFTQALRQD 284
                                    11        21        31        41        51        61  |     71        81|       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    |  261       271       281   
                                   10-MSE                                                64-MSE            82-MSE                                                                                                    189-MSE                                                            256-MSE                        
                                                                                                                                                                                                                                                                                            260-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 1YDN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YDN)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8YEF2_BRUME | Q8YEF2)
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:0004419    hydroxymethylglutaryl-CoA lyase activity    Catalysis of the reaction: (S)-3-hydroxy-3-methylglutaryl-CoA = acetoacetate + acetyl-CoA.
    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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

lr35
1ydo