Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID
 
Authors :  E. K. Jaffe, J. Kervinen, J. Martins, F. Stauffer, R. Neier, A. Wlodawer
Date :  13 Mar 02  (Deposition) - 17 Apr 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Dehydratase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. K. Jaffe, J. Kervinen, J. Martins, F. Stauffer, R. Neier, A. Wlodawer, A. Zdanov
Species-Specific Inhibition Of Porphobilinogen Synthase By 4-Oxosebacic Acid
J. Biol. Chem. V. 277 19792 2002
PubMed-ID: 11909869  |  Reference-DOI: 10.1074/JBC.M201486200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PORPHOBILINOGEN SYNTHASE
    Chains: A, B
    EC Number: 4.2.1.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DELTA-AMINOLEVULINIC ACID DEHYDRATASE, 5-AMINOLEVULINIC ACID DEHYDRATASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2DSB2Ligand/Ion4,7-DIOXOSEBACIC ACID
3MG2Ligand/IonMAGNESIUM ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1CME8Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2DSB8Ligand/Ion4,7-DIOXOSEBACIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:119 , CYS A:121 , CYS A:129 , HOH A:685BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWAREGLU A:231 , HOH A:403 , HOH A:422 , HOH A:433 , HOH A:439 , HOH A:483BINDING SITE FOR RESIDUE MG A 401
3AC3SOFTWARECYS B:119 , CYS B:121 , CYS B:129 , HOH B:686BINDING SITE FOR RESIDUE ZN B 400
4AC4SOFTWAREGLU B:231 , HOH B:412 , HOH B:421 , HOH B:427 , HOH B:430 , HOH B:448BINDING SITE FOR RESIDUE MG B 401
5AC5SOFTWARESER A:164 , LYS A:194 , PHE A:199 , TYR A:200 , PHE A:203 , ARG A:204 , ARG A:215 , GLN A:219 , LYS A:246 , TYR A:269 , VAL A:271 , SER A:272 , TYR A:311 , HOH A:463BINDING SITE FOR RESIDUE DSB A 350
6AC6SOFTWARESER B:164 , TYR B:191 , LYS B:194 , PHE B:199 , TYR B:200 , PHE B:203 , ARG B:204 , ARG B:215 , GLN B:219 , LYS B:246 , TYR B:269 , VAL B:271 , SER B:272 , TYR B:311 , HOH B:511 , HOH B:686BINDING SITE FOR RESIDUE DSB B 350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L6S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:246 -Pro A:247
2Lys B:246 -Pro B:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L6S)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_ECOLI240-252
 		  2A:239-251
B:239-251
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_ECOLI240-252
 		  8A:239-251
B:239-251

(-) Exons   (0, 0)

(no "Exon" information available for 1L6S)

(-) 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:323
 aligned with HEM2_ECOLI | P0ACB2 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    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       291       301       311       321   
           HEM2_ECOLI     2 TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLCEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 324
               SCOP domains d1l6sa_ A: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1l6sA00 A:1-323 Aldolase class I                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh....hhh.eeeeeeee......ee.......eeee..hhhhhhhhhhhh...eeeeeee.......hhhhhh..hhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....ee....ee.....hhhhhhhhh...............hhhhhhhhhhhhhhh....eeee....hhhhhhhhhh.....eeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeee.hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l6s A   1 TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLcEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 323
                                    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   
                                                                                                                                                              133-CME                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:323
 aligned with HEM2_ECOLI | P0ACB2 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    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       291       301       311       321   
           HEM2_ECOLI     2 TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLCEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 324
               SCOP domains d1l6sb_ B: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1l6sB00 B:1-323 Aldolase class I                                                                                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) -ALAD-1l6sB01 B:2-320                                                                                                                                                                                                                                                                                                           --- Pfam domains (1)
           Pfam domains (2) -ALAD-1l6sB02 B:2-320                                                                                                                                                                                                                                                                                                           --- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhh.....hhh.eeeeeeee......ee.......eeee..hhhhhhhhhhhh...eeeeeee.......hhhhhh..hhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh.....ee....ee.....hhhhhhhhh...............hhhhhhhhhhhhhhh....eeee....hhhhhhhhhh.....eeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eee..hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l6s B   1 TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLcEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 323
                                    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   
                                                                                                                                                              133-CME
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HEM2_ECOLI | P0ACB2)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004655    porphobilinogen synthase activity    Catalysis of the reaction: 2 5-aminolevulinate = 2 H(2)O + H(+) + porphobilinogen.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006783    heme biosynthetic process    The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
    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.
    GO:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
    GO:0006782    protoporphyrinogen IX biosynthetic process    The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
    GO:0033014    tetrapyrrole biosynthetic process    The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
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.

 Visualization

(-) Interactive Views

Asymmetric 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
    CME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DSB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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
    Lys A:246 - Pro A:247   [ RasMol ]  
    Lys B:246 - Pro B:247   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1l6s
    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
  HEM2_ECOLI | P0ACB2
    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)
  4.2.1.24
    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
  HEM2_ECOLI | P0ACB2
    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
        HEM2_ECOLI | P0ACB2: 1b4e 1i8j 1l6y 5mhb

(-) Related Entries Specified in the PDB File

1i8j 1I8J CONTAINS PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID
1l6y 1L6Y CONTAINS PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4-OXOSEBACIC ACID