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

(-) Description

Authors :  Y. P. Nieh, J. Raftery, S. Weisgerber, J. Habash, F. Schotte, T. Ursby, M A. Haedener, J. W. Campbell, Q. Hao, J. R. Helliwell
Date :  11 Jan 99  (Deposition) - 02 Feb 99  (Release) - 18 Sep 13  (Revision)
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Biosynthesis Of Linear Tetrapyrrole, All Alpha/Beta, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  Y. P. Nieh, J. Raftery, S. Weisgerber, J. Habash, F. Schotte, T. Ursby, M. Wulff, A. Haedener, J. W. Campbell, Q. Hao, J. R. Helliwell
Accurate And Highly Complete Synchrotron Protein Crystal Laue Diffraction Data Using The Esrf Ccd And The Daresbury Laue Software
J. Synchrotron Radiat. V. 6 995 1999
PubMed: search

(-) Compounds

    EC Number2.5.1.61
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
1AC1SOFTWARESER A:81 , LYS A:83 , ASP A:84 , THR A:127 , SER A:128 , SER A:129 , ARG A:131 , ARG A:132 , LEU A:148 , ARG A:155 , LEU A:169 , ALA A:170 , GLN A:198 , GLY A:199 , CYS A:242 , HOH A:325 , HOH A:328 , HOH A:331 , HOH A:342 , HOH A:343 , HOH A:442BINDING SITE FOR RESIDUE DPM A 314

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1PORPHOBILINOGEN_DEAMPS00533 Porphobilinogen deaminase cofactor-binding site.HEM3_ECOLI231-247  1A:231-247

(-) Exons   (0, 0)

(no "Exon" information available for 2YPN)

(-) 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:294
 aligned with HEM3_ECOLI | P06983 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:311
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312 
               SCOP domains d2ypna1 A:3-219 Porphobilinogen deaminas                 e (hydroxymethylbilane synthase), N-terminal domain                                                                                                             d2ypna2 A:220-313 Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain  SCOP domains
               CATH domains 2ypnA01 A:3-99,A:200-220 Periplasmic bin                 ding protein-like II                    2ypnA02 A:100-199 Periplasmic binding protein-like II                                               2ypnA01              2ypnA03 A:221-306  [code=, no name defined]                                ------- CATH domains
               Pfam domains --Porphobil_deam-2ypnA02 A:5-217                                                                                                                                                                                       -------Porphobil_deamC-2ypnA01 A:225-296                                       ----------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhh....eeeeee..-----------------.hhhhhhhhhhh.....eeeeehhh........eeeeee.......eeeee.............eee...hhhhhhhhhh....eee.....hhhhhhhhh.....eeeeehhhhhh...hhheeeee.............eeeeee...hhhhhhhhhh..hhhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeeee......eeeeeeeeehhhhhhhhhhhhhhhhhh.hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PORPHOBILINOGEN_D------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                    12        22        32        42         -       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312 
                                                                  42                60                                                                                                                                                                                                                                                             

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HEM3_ECOLI | P06983)
molecular function
    GO:0004418    hydroxymethylbilane synthase activity    Catalysis of the reaction: H(2)O + 4 porphobilinogen = hydroxymethylbilane + 4 NH(4)(+).
    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.
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:0018160    peptidyl-pyrromethane cofactor linkage    The covalent binding of a pyrromethane (dipyrrin) cofactor to protein via the sulfur atom of cysteine forming dipyrrolylmethanemethyl-L-cysteine.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.


(-) 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)
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
(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
    DPM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AC1  [ RasMol ]  +environment [ RasMol ]
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ypn)

(-) Still Images

  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
Access by UniProt ID/Accession number
  HEM3_ECOLI | P06983
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
Access by Enzyme Classificator   (EC Number)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
Access by UniProt ID/Accession number
  HEM3_ECOLI | P06983
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        HEM3_ECOLI | P069831ah5 1gtk 1pda 1ypn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YPN)