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(-) Description

Title :  ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN
 
Authors :  V. -M. Leppanen, M. C. Merckel, D. L. Ollis, K. K. Wong, J. W. Kozarich, A. Goldman
Date :  19 May 99  (Deposition) - 24 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyruvate Formate Lyase, Anaerobic, X-Ray Crystallography, Homodimer, Enzyme Mechanism, Lyase/Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. M. Leppanen, M. C. Merckel, D. L. Ollis, K. K. Wong, J. W. Kozarich, A. Goldman
Pyruvate Formate Lyase Is Structurally Homologous To Type I Ribonucleotide Reductase.
Structure Fold. Des. V. 7 733 1999
PubMed-ID: 10425676  |  Reference-DOI: 10.1016/S0969-2126(99)80098-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE FORMATE-LYASE
    Cellular LocationCYTOPLASM
    ChainsA, B
    EC Number2.3.1.54
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System GenePFL
    Expression System PlasmidPKK-TRYPFL
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 1-624
    GenePFL
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPFL

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QHM)

(-) Sites  (0, 0)

(no "Site" information available for 1QHM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QHM)

(-) 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:612
 aligned with PFLB_ECOLI | P09373 from UniProtKB/Swiss-Prot  Length:760

    Alignment length:612
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614  
          PFLB_ECOLI      5 NEKLATAWEGFTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVMEGVKLENRTHAPVDFDTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIEGSCKAYNRELDPMIKKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIGDYRRVALYGIDYLMKDKLAQFTSLQADLENGVNLEQTIRLREEIAEQHRALGQMKEMAAKYGYDISGPATNAQEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQEAQEMVDHLVMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNTLYTMGPSPEPNMTILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACCVSPMIVGKQMQFFGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERMDHFMDWLAKQYITALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIKYAKVKPIRDEDGLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIPTQSVLTITSNVVYGKK  616
               SCOP domains d1qhma_ A: Pyruvate formate-lyase, PFL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1qhmA00 A:1004-1615  [code=3.20.70.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh.......hhh....hhhhhhh........hhh.....hhhhhhhhhhhhhhhhhhhh....eeeeeee...........................eeee.hhh.hhhhhhhhhh......hhhhhhhhh....hhhhhhhh..hhhhhhhhh..ee..............hhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh......hhh............eeee...........hhhhhhhhhhhh........eeeee.....hhhhhhhhhhhhhh...eeeehhhhhhhh....ee.......ee...eeeee..eeehhhhhhhhh...ee....ee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.....eeeeee.ee.hhhhhhhhhhhhh.eeeeee.....eeeeeee..........hhhhhhhhhhhhhhhhhhhh...hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1qhm A 1004 NEKLATAWEGFTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVMEGVKLENRTHAPVDFDTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIEGSCKAYNRELDPMIKKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIGDYRRVALYGIDYLMKDKLAQFTSLQADLENGVNLEQTIRLREEIAEQHRALGQMKEMAAKYGYDISGPATNAQEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQEAQEMVDHLVMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNTLYTMGPSPEPNMTILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACCVSPMIVGKQMQFFGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERMDHFMDWLAKQYITALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIKYAKVKPIRDEDGLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIPTQSVLTITSNVVYGKK 1615
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483      1493      1503      1513      1523      1533      1543      1553      1563      1573      1583      1593      1603      1613  

Chain B from PDB  Type:PROTEIN  Length:612
 aligned with PFLB_ECOLI | P09373 from UniProtKB/Swiss-Prot  Length:760

    Alignment length:612
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614  
          PFLB_ECOLI      5 NEKLATAWEGFTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVMEGVKLENRTHAPVDFDTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIEGSCKAYNRELDPMIKKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIGDYRRVALYGIDYLMKDKLAQFTSLQADLENGVNLEQTIRLREEIAEQHRALGQMKEMAAKYGYDISGPATNAQEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQEAQEMVDHLVMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNTLYTMGPSPEPNMTILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACCVSPMIVGKQMQFFGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERMDHFMDWLAKQYITALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIKYAKVKPIRDEDGLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIPTQSVLTITSNVVYGKK  616
               SCOP domains d1qhmb_ B: Pyruvate formate-lyase, PFL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1qhmB00 B:2004-2615  [code=3.20.70.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) --------PFL-1qhmB01 B:2012-2613                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) --------PFL-1qhmB02 B:2012-2613                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   -- Pfam domains (2)
         Sec.struct. author .hhhhhhh......hhh....hhhhhhh........hhh.....hhhhhhhhhhhhhhhhhhhh....eeeeeee............hhh............eeee.hhh.hhhhhhhhhh......hhhhhhhhh....hhhhhhhh..hhhhhhhhh..ee..............hhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.....................eeee...........hhhhhhhhhhhh........eeeee.....hhhhhhhhhhhhhh...eeeehhhhhhhh....ee.......ee...eeeee..eeehhhhhhhhh...ee....ee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.....eeeeee.ee.hhhhhhhhhhhhheeeeee........eeeeee.........hhhhhhhhhhhhhhhhhhhh...hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1qhm B 2004 NEKLATAWEGFTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVMEGVKLENRTHAPVDFDTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIEGSCKAYNRELDPMIKKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIGDYRRVALYGIDYLMKDKLAQFTSLQADLENGVNLEQTIRLREEIAEQHRALGQMKEMAAKYGYDISGPATNAQEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQEAQEMVDHLVMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNTLYTMGPSPEPNMTILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACCVSPMIVGKQMQFFGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERMDHFMDWLAKQYITALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIKYAKVKPIRDEDGLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIPTQSVLTITSNVVYGKK 2615
                                  2013      2023      2033      2043      2053      2063      2073      2083      2093      2103      2113      2123      2133      2143      2153      2163      2173      2183      2193      2203      2213      2223      2233      2243      2253      2263      2273      2283      2293      2303      2313      2323      2333      2343      2353      2363      2373      2383      2393      2403      2413      2423      2433      2443      2453      2463      2473      2483      2493      2503      2513      2523      2533      2543      2553      2563      2573      2583      2593      2603      2613  

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PFL-like (29)
(-)
Family: PFL (6)
1aPFL-1qhmB01B:2012-2613
1bPFL-1qhmB02B:2012-2613

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PFLB_ECOLI | P09373)
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:0008861    formate C-acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + formate = CoA + pyruvate.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    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:0006567    threonine catabolic process    The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PFLB_ECOLI | P093731cm5 1h16 1h17 1h18 1mzo 2pfl 3pfl

(-) Related Entries Specified in the PDB File

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