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(-) Description

Title :  2.01 ANGSTROM X-RAY CRYSTAL STRUCTURE OF A MIXED DISULFIDE BETWEEN COENZYME M AND NADPH-DEPENDENT OXIDOREDUCTASE 2-KETOPROPYL COENZYME M CARBOXYLASE
 
Authors :  A. S. Pandey, B. Nocek, D. D. Clark, S. A. Ensign, J. W. Peters
Date :  05 Oct 05  (Deposition) - 12 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Mixed Disulfide, Coenzyme M, Redox-Active Center, Fad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Pandey, B. Nocek, D. D. Clark, S. A. Ensign, J. W. Peters
Mechanistic Implications Of The Structure Of The Mixed-Disulfide Intermediate Of The Disulfide Oxidoreductase, 2-Ketopropyl-Coenzyme M Oxidoreductase/Carboxylase.
Biochemistry V. 45 113 2006
PubMed-ID: 16388586  |  Reference-DOI: 10.1021/BI051518O

(-) Compounds

Molecule 1 - 2-OXOPROPYL-COM REDUCTASE
    Atcc: 35674
    Chains: A, B
    EC Number: 1.8.1.5
    Organism Scientific: XANTHOBACTER AUTOTROPHICUS
    Organism Taxid: 78245
    Strain: PY2
    Synonym: NADPH:2-KETOPROPYL COENZYME M CARBOXYLASE/ OXIDOREDUCTASE, 2-KPCC, ALIPHATIC EPOXIDE CARBOXYLATION COMPONENT II

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ACN2Ligand/IonACETONE
2COM2Ligand/Ion1-THIOETHANESULFONIC ACID
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:53 , ARG A:56 , PHE A:57 , GLY A:79 , CYS A:82 , PRO A:83 , MET A:140 , MET A:361 , ARG A:365 , HOH A:2088 , ACN B:1525BINDING SITE FOR RESIDUE COM A1000
2AC2SOFTWAREGLY A:50 , GLY A:52 , ALA A:53 , ALA A:54 , ASP A:73 , ARG A:74 , TRP A:75 , GLY A:80 , SER A:81 , ALA A:86 , CYS A:87 , HIS A:90 , HIS A:91 , PRO A:157 , ALA A:158 , ALA A:181 , VAL A:182 , GLY A:183 , HIS A:202 , TYR A:229 , GLY A:352 , ASP A:353 , MET A:359 , GLU A:360 , MET A:361 , ALA A:364 , NAP A:1526 , HOH A:2050 , HOH A:2055 , HOH A:2102 , HOH A:2252 , HOH A:2253 , HOH A:2258 , HOH A:2364 , HOH A:2365 , HOH A:2366 , PHE B:501BINDING SITE FOR RESIDUE FAD A1524
3AC3SOFTWARELEU A:189 , GLY A:222 , SER A:223 , LYS A:224 , THR A:225 , GLU A:228 , ARG A:245 , THR A:246 , LYS A:250 , LEU A:312 , GLY A:313 , MET A:359 , GLU A:360 , FAD A:1524 , HOH A:2368 , HOH A:2369 , HOH A:2370 , HOH A:2371 , HOH A:2372 , HOH A:2373 , HOH A:2374 , HOH A:2375BINDING SITE FOR RESIDUE NAP A1526
4AC4SOFTWAREACN A:1525 , HOH A:2367 , ALA B:53 , ARG B:56 , PHE B:57 , GLY B:79 , CYS B:82 , PRO B:83 , MET B:140 , MET B:361 , ARG B:365BINDING SITE FOR RESIDUE COM B1000
5AC5SOFTWAREPHE A:501 , GLY B:50 , GLY B:52 , ALA B:53 , ALA B:54 , VAL B:72 , ASP B:73 , ARG B:74 , TRP B:75 , GLY B:80 , SER B:81 , ALA B:86 , CYS B:87 , HIS B:90 , HIS B:91 , PRO B:157 , ALA B:158 , ALA B:181 , VAL B:182 , GLY B:183 , HIS B:202 , TYR B:229 , GLY B:352 , ASP B:353 , MET B:359 , GLU B:360 , MET B:361 , ALA B:364 , NAP B:1526 , HOH B:2035 , HOH B:2326 , HOH B:2327 , HOH B:2328 , HOH B:2329 , HOH B:2330BINDING SITE FOR RESIDUE FAD B1524
6AC6SOFTWAREHIS B:90 , LEU B:189 , GLY B:222 , SER B:223 , LYS B:224 , THR B:225 , GLU B:228 , ARG B:245 , THR B:246 , LYS B:250 , GLY B:311 , LEU B:312 , GLY B:313 , MET B:359 , GLU B:360 , PHE B:390 , FAD B:1524 , HOH B:2122 , HOH B:2187 , HOH B:2332 , HOH B:2333 , HOH B:2334 , HOH B:2335 , HOH B:2336BINDING SITE FOR RESIDUE NAP B1526
7AC7SOFTWAREPHE A:501 , HIS A:506 , GLN A:509 , HOH A:2367 , ARG B:365 , COM B:1000BINDING SITE FOR RESIDUE ACN A1525
8AC8SOFTWAREARG A:365 , COM A:1000 , HOH A:2088 , LEU B:431 , PHE B:501 , HIS B:506 , GLN B:509 , HOH B:2331BINDING SITE FOR RESIDUE ACN B1525

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C3C)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:357 -Pro A:358
2Met A:419 -Pro A:420
3Leu A:431 -Pro A:432
4Phe A:501 -Leu A:502
5Gly B:357 -Pro B:358
6Met B:419 -Pro B:420
7Leu B:431 -Pro B:432
8Phe B:501 -Leu B:502

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C3C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C3C)

(-) Exons   (0, 0)

(no "Exon" information available for 2C3C)

(-) 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:522
 aligned with XECC_XANP2 | Q56839 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:522
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521  
           XECC_XANP2     2 KVWNARNDHLTINQWATRIDEILEAPDGGEVIYNVDENDPREYDAIFIGGGAAGRFGSAYLRAMGGRQLIVDRWPFLGGSCPHNACVPHHLFSDCAAELMLARTFSGQYWFPDMTEKVVGIKEVVDLFRAGRNGPHGIMNFQSKEQLNLEYILNCPAKVIDNHTVEAAGKVFKAKNLILAVGAGPGTLDVPGVNAKGVFDHATLVEELDYEPGSTVVVVGGSKTAVEYGCFFNATGRRTVMLVRTEPLKLIKDNETRAYVLDRMKEQGMEIISGSNVTRIEEDANGRVQAVVAMTPNGEMRIETDFVFLGLGEQPRSAELAKILGLDLGPKGEVLVNEYLQTSVPNVYAVGDLIGGPMEMFKARKSGCYAARNVMGEKISYTPKNYPDFLHTHYEVSFLGMGEEEARAAGHEIVTIKMPPDTENGLNVALPASDRTMLYAFGKGTAHMSGFQKIVIDAKTRKVLGAHHVGYGAKDAFQYLNVLIKQGLTVDELGDMDELFLNPTHFIQLSRLRAGSKNLVSL 523
               SCOP domains d2c3ca1 A:2-192,A:314-383 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                                                                                    d2c3ca2 A:193-313 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                      d2c3ca1 A:2-192,A:314-383                                             d2c3ca3 A:384-523 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                                          SCOP domains
               CATH domains 2c3cA01 A:2-85,A:132-186,A:314-378  [code=3.50.50.60, no name defined]              -2c3cA02 A:87-131,A:197-244,A:270-311         2c3cA01 A:2-85,A:132-186,A:314-378                     ----------2c3cA02 A:87-131,A:197-244,A:270-311            ---------2c3cA03        -2c3cA02 A:87-131,A:197-244,A:270-311      --2c3cA01 A:2-85,A:132-186,A:314-378                               -------2c3cA03 A:254-268,A:386-523  [code=3.30.390.30, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......hhhhhhhhhhhhhhh.....eeee..........eeee..hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee....eeee..eeee..eeee...eee...eee............eeehhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh..eee...eeeeeee.....eeeeeeee..eeeeee...eee...eee.hhhhhhhhh.....................eee.hhhhh...hhhhhhhhhhhhhhhhh............eeee...eeeeee.hhhhhhhh...eeeeee.................hhhhhhh..hhhhhheeeeeee.....eeeeeeee..hhhhhhhhhhhhhh..hhhhhhh.........hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c3c A   2 KVWNARNDHLTINQWATRIDEILEAPDGGEVIYNVDENDPREYDAIFIGGGAAGRFGSAYLRAMGGRQLIVDRWPFLGGSCPHNACVPHHLFSDCAAELMLARTFSGQYWFPDMTEKVVGIKEVVDLFRAGRNGPHGIMNFQSKEQLNLEYILNCPAKVIDNHTVEAAGKVFKAKNLILAVGAGPGTLDVPGVNAKGVFDHATLVEELDYEPGSTVVVVGGSKTAVEYGCFFNATGRRTVMLVRTEPLKLIKDNETRAYVLDRMKEQGMEIISGSNVTRIEEDANGRVQAVVAMTPNGEMRIETDFVFLGLGEQPRSAELAKILGLDLGPKGEVLVNEYLQTSVPNVYAVGDLIGGPMEMFKARKSGCYAARNVMGEKISYTPKNYPDFLHTHYEVSFLGMGEEEARAAGHEIVTIKMPPDTENGLNVALPASDRTMLYAFGKGTAHMSGFQKIVIDAKTRKVLGAHHVGYGAKDAFQYLNVLIKQGLTVDELGDMDELFLNPTHFIQLSRLRAGSKNLVSL 523
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521  


Chain B from PDB  Type:PROTEIN  Length:522
 aligned with XECC_XANP2 | Q56839 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:522
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521  
           XECC_XANP2     2 KVWNARNDHLTINQWATRIDEILEAPDGGEVIYNVDENDPREYDAIFIGGGAAGRFGSAYLRAMGGRQLIVDRWPFLGGSCPHNACVPHHLFSDCAAELMLARTFSGQYWFPDMTEKVVGIKEVVDLFRAGRNGPHGIMNFQSKEQLNLEYILNCPAKVIDNHTVEAAGKVFKAKNLILAVGAGPGTLDVPGVNAKGVFDHATLVEELDYEPGSTVVVVGGSKTAVEYGCFFNATGRRTVMLVRTEPLKLIKDNETRAYVLDRMKEQGMEIISGSNVTRIEEDANGRVQAVVAMTPNGEMRIETDFVFLGLGEQPRSAELAKILGLDLGPKGEVLVNEYLQTSVPNVYAVGDLIGGPMEMFKARKSGCYAARNVMGEKISYTPKNYPDFLHTHYEVSFLGMGEEEARAAGHEIVTIKMPPDTENGLNVALPASDRTMLYAFGKGTAHMSGFQKIVIDAKTRKVLGAHHVGYGAKDAFQYLNVLIKQGLTVDELGDMDELFLNPTHFIQLSRLRAGSKNLVSL 523
               SCOP domains d2c3cb1 B:2-192,B:314-383 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                                                                                    d2c3cb2 B:193-313 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                      d2c3cb1 B:2-192,B:314-383                                             d2c3cb3 B:384-523 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                                          SCOP domains
               CATH domains 2c3cB01 B:2-85,B:132-186,B:314-378  [code=3.50.50.60, no name defined]              -2c3cB02 B:87-131,B:197-244,B:270-311         2c3cB01 B:2-85,B:132-186,B:314-378                     ----------2c3cB02 B:87-131,B:197-244,B:270-311            ---------2c3cB03        -2c3cB02 B:87-131,B:197-244,B:270-311      --2c3cB01 B:2-85,B:132-186,B:314-378                               -------2c3cB03 B:254-268,B:386-523  [code=3.30.390.30, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......hhhhhhhhhhhhhh......eeee..........eeee..hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee....eeee..eeee..eeee...eee...eee............eeehhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh..eee...eeeeeee.....eeeeeeee..eeeeee...eee...eee.hhhhhhhhh.....................eee.hhhhh...hhhhhhhhhhhhhhhhh............eeee...eeeeee.hhhhhhhh...eeeeee.................hhhhhhh..hhhhh.eeeeeee.....eeeeeeee..hhhhhhhhhhhhhh..hhhhhhh.........hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c3c B   2 KVWNARNDHLTINQWATRIDEILEAPDGGEVIYNVDENDPREYDAIFIGGGAAGRFGSAYLRAMGGRQLIVDRWPFLGGSCPHNACVPHHLFSDCAAELMLARTFSGQYWFPDMTEKVVGIKEVVDLFRAGRNGPHGIMNFQSKEQLNLEYILNCPAKVIDNHTVEAAGKVFKAKNLILAVGAGPGTLDVPGVNAKGVFDHATLVEELDYEPGSTVVVVGGSKTAVEYGCFFNATGRRTVMLVRTEPLKLIKDNETRAYVLDRMKEQGMEIISGSNVTRIEEDANGRVQAVVAMTPNGEMRIETDFVFLGLGEQPRSAELAKILGLDLGPKGEVLVNEYLQTSVPNVYAVGDLIGGPMEMFKARKSGCYAARNVMGEKISYTPKNYPDFLHTHYEVSFLGMGEEEARAAGHEIVTIKMPPDTENGLNVALPASDRTMLYAFGKGTAHMSGFQKIVIDAKTRKVLGAHHVGYGAKDAFQYLNVLIKQGLTVDELGDMDELFLNPTHFIQLSRLRAGSKNLVSL 523
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C3C)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (XECC_XANP2 | Q56839)
molecular function
    GO:0050628    2-oxopropyl-CoM reductase (carboxylating) activity    Catalysis of the reaction: acetoacetate + coenzyme M + NADP(+) = 2-oxopropyl-coenzyme M + CO(2) + NADPH.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0042208    propylene catabolic process    The chemical reactions and pathways resulting in the breakdown of propylene, an alkene produced by catalytic or thermal cracking of hydrocarbons or as a by-product of petroleum refining.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XECC_XANP2 | Q56839: 1mo9 1mok 2c3d 3q6j

(-) Related Entries Specified in the PDB File

1mo9 NADPH DEPENDENT 2-KETOPROPYL COENZYME MOXIDOREDUCTASE/CARBOXYLASE COMPLEXED WITH 2- KETOPROPYLCOENZYME M
1mok NADPH DEPENDENT 2-KETOPROPYL COENZYME MOXIDOREDUCTASE/CARBOXYLASE
2c3d 2.15 ANGSTROM CRYSTAL STRUCTURE OF 2- KETOPROPYL COENZYME M OXIDOREDUCTASE CARBOXYLASE WITH A COENZYME M DISULFIDE BOUND AT THE ACTIVE SITE