Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HMG-COA SYNTHASE FROM ENTEROCOCCUS FAECALIS WITH ACETOACETYL-COA LIGAND.
 
Authors :  C. N. Steussy, A. A. Vartia, J. W. Burgner Ii, A. Sutherlin, V. W. Rodwel C. V. Stauffacher
Date :  08 Feb 05  (Deposition) - 08 Nov 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thiolase Family, Coenzymea, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. N. Steussy, A. A. Vartia, J. W. Burgner Ii, A. Sutherlin, V. W. Rodwell, C. V. Stauffacher
X-Ray Crystal Structures Of Hmg-Coa Synthase From Enterococcus Faecalis And A Complex With Its Second Substrate/Inhibitor Acetoacetyl-Coa.
Biochemistry V. 44 14256 2005
PubMed-ID: 16245942  |  Reference-DOI: 10.1021/BI051487X

(-) Compounds

Molecule 1 - HMG-COA SYNTHASE
    Chains: A
    EC Number: 4.1.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21[DE3]
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
 
Molecule 2 - HMG-COA SYNTHASE
    Chains: B
    EC Number: 4.1.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21[DE3]
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1AAE1Ligand/IonACETOACETIC ACID
2COA1Ligand/IonCOENZYME A
3CSD2Mod. Amino Acid3-SULFINOALANINE
4GOL2Ligand/IonGLYCEROL
5SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:7 , THR A:64 , ARG A:167BINDING SITE FOR RESIDUE SO4 A 602
2AC2SOFTWAREASP A:83 , THR A:377 , VAL A:378 , ARG A:379 , HOH A:650 , HOH A:654 , HOH A:720 , TYR B:183 , PRO B:188BINDING SITE FOR RESIDUE GOL A 604
3AC3SOFTWARELYS B:7 , THR B:64 , ARG B:167 , HOH B:707 , HOH B:772 , HOH B:818BINDING SITE FOR RESIDUE SO4 B 603
4AC4SOFTWAREALA A:254 , ASP B:29 , GLY B:31 , LYS B:32 , GLY B:36 , TYR B:143 , GLY B:148 , GLY B:149 , THR B:152 , VAL B:196 , SER B:201 , ASN B:202 , PRO B:235 , TYR B:236 , MET B:239 , LYS B:242 , AAE B:611 , HOH B:778 , HOH B:829 , HOH B:858BINDING SITE FOR RESIDUE COA B 601
5AC5SOFTWARECYS B:111 , TYR B:143 , PHE B:185 , HIS B:233 , ASN B:275 , TYR B:277 , SER B:308 , COA B:601 , HOH B:814 , HOH B:858BINDING SITE FOR RESIDUE AAE B 611
6AC6SOFTWARETYR A:183 , PRO A:188 , ILE B:82 , ASP B:83 , THR B:377 , ARG B:379 , HOH B:651 , HOH B:855BINDING SITE FOR RESIDUE GOL B 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:309 -Ala A:310
2Gly B:309 -Ala B:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YSL)

(-) 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:383
 aligned with HMGCS_ENTFL | Q9FD71 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:383
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380   
          HMGCS_ENTFL     1 MTIGIDKISFFVPPYYIDMTALAEARNVDPGKFHIGIGQDQMAVNPISQDIVTFAANAAEAILTKEDKEAIDMVIVGTESSIDESKAAAVVLHRLMGIQPFARSFEIKEACYGATAGLQLAKNHVALHPDKKVLVVAADIAKYGLNSGGEPTQGAGAVAMLVASEPRILALKEDNVMLTQDIYDFWRPTGHPYPMVDGPLSNETYIQSFAQVWDEHKKRTGLDFADYDALAFHIPYTKMGKKALLAKISDQTEAEQERILARYEESIIYSRRVGNLYTGSLYLGLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELSIAEYEAMFAETLDTDIDQTLEDELKYSISAINNTVRSYRN 383
               SCOP domains d1ysla1 A:1-167 automated matches                                                                                                                                      d1ysla2 A:168-383 automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...eeeehhhhhhhh..............eeee.....hhhhhhhhhhhh..hhhhhhheeeeeee.........hhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.......hhhhheeeeeeeeeee....eee....eeee.....ee........eehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeeee..hhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhh.......ee........eeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ysl A   1 MTIGIDKISFFVPPYYIDMTALAEARNVDPGKFHIGIGQDQMAVNPISQDIVTFAANAAEAILTKEDKEAIDMVIVGTESSIDESKAAAVVLHRLMGIQPFARSFEIKEAcYGATAGLQLAKNHVALHPDKKVLVVAADIAKYGLNSGGEPTQGAGAVAMLVASEPRILALKEDNVMLTQDIYDFWRPTGHPYPMVDGPLSNETYIQSFAQVWDEHKKRTGLDFADYDALAFHIPYTKMGKKALLAKISDQTEAEQERILARYEESIIYSRRVGNLYTGSLYLGLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELSIAEYEAMFAETLDTDIDQTLEDELKYSISAINNTVRSYRN 383
                                    10        20        30        40        50        60        70        80        90       100       110|      120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380   
                                                                                                                                        111-CSD                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:383
 aligned with HMGCS_ENTFL | Q9FD71 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:383
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380   
          HMGCS_ENTFL     1 MTIGIDKISFFVPPYYIDMTALAEARNVDPGKFHIGIGQDQMAVNPISQDIVTFAANAAEAILTKEDKEAIDMVIVGTESSIDESKAAAVVLHRLMGIQPFARSFEIKEACYGATAGLQLAKNHVALHPDKKVLVVAADIAKYGLNSGGEPTQGAGAVAMLVASEPRILALKEDNVMLTQDIYDFWRPTGHPYPMVDGPLSNETYIQSFAQVWDEHKKRTGLDFADYDALAFHIPYTKMGKKALLAKISDQTEAEQERILARYEESIIYSRRVGNLYTGSLYLGLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELSIAEYEAMFAETLDTDIDQTLEDELKYSISAINNTVRSYRN 383
               SCOP domains d1yslb1 B:1-167 automated matches                                                                                                                                      d1yslb2 B:168-383 automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...eeeehhhhhhhh..hhhhhhh.....eeee.....hhhhhhhhhhhh..hhhhhhheeeeeee.........hhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.......hhhhheeeeeeeeeee....eee....eeee.....ee........eehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeeee..hhhhh.hhhhhhhhhhh.ee.hhhhhhhhhhh.......ee........eeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ysl B   1 MTIGIDKISFFVPPYYIDMTALAEARNVDPGKFHIGIGQDQMAVNPISQDIVTFAANAAEAILTKEDKEAIDMVIVGTESSIDESKAAAVVLHRLMGIQPFARSFEIKEACYGATAGLQLAKNHVALHPDKKVLVVAADIAKYGLNSGGEPTQGAGAVAMLVASEPRILALKEDNVMLTQDIYDFWRPTGHPYPMVDGPLSNETYIQSFAQVWDEHKKRTGLDFADYDALAFHIPYTKMGKKALLAKISDQTEAEQERILARYEESIIYSRRVGNLYTGSLYLGLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELSIAEYEAMFAETLDTDIDQTLEDELKYSISAINNTVRSYRN 383
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YSL)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HMGCS_ENTFL | Q9FD71)
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:0004421    hydroxymethylglutaryl-CoA synthase activity    Catalysis of the reaction: acetoacetyl-CoA + acetyl-CoA + H(2)O = (S)-3-hydroxy-3-methylglutaryl-CoA + CoA + H(+).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AAE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    COA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CSD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:309 - Ala A:310   [ RasMol ]  
    Gly B:309 - Ala B:310   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ysl
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HMGCS_ENTFL | Q9FD71
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.3.5
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  HMGCS_ENTFL | Q9FD71
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HMGCS_ENTFL | Q9FD71: 1x9e 2hdb 3v4n 3v4x

(-) Related Entries Specified in the PDB File

1x9e NATIVE STRUCTURE OF HMG-COA SYNTHASE FROM ENTEROCOCCUS FAECALIS