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(-) Description

Title :  STRUCTURAL BASIS FOR CARBON DIOXIDE BINDING BY 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/CARBOXYLASE
 
Authors :  A. S. Pandey, D. W. Mulder, S. A. Ensign, J. W. Peters
Date :  01 Jan 11  (Deposition) - 16 Feb 11  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Disulfide, Carbon Dioxide, Coenzyme M, Fad, Nadp, Oxidoreductase, Carboxylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Pandey, D. W. Mulder, S. A. Ensign, J. W. Peters
Structural Basis For Carbon Dioxide Binding By 2-Ketopropyl Coenzyme M Oxidoreductase/Carboxylase.
Febs Lett. V. 585 459 2011
PubMed-ID: 21192936  |  Reference-DOI: 10.1016/J.FEBSLET.2010.12.035

(-) Compounds

Molecule 1 - 2-OXOPROPYL-COM REDUCTASE, CARBOXYLATING
    Chains: A, B
    EC Number: 1.8.1.5
    Organism Scientific: XANTHOBACTER AUTOTROPHICUS
    Organism Taxid: 78245
    Strain: PY2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 12)

Asymmetric/Biological Unit (8, 12)
No.NameCountTypeFull Name
1ACN1Ligand/IonACETONE
2BCT2Ligand/IonBICARBONATE ION
3CO21Ligand/IonCARBON DIOXIDE
4COM1Ligand/Ion1-THIOETHANESULFONIC ACID
5FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
6KPC1Ligand/Ion(2-[2-KETOPROPYLTHIO]ETHANESULFONATE
7MG2Ligand/IonMAGNESIUM ION
8NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:90 , LEU 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 , GLY A:311 , LEU A:312 , GLY A:313 , MET A:359 , GLU A:360 , HOH A:567 , HOH A:634 , HOH A:667 , HOH A:672 , HOH A:742 , HOH A:951 , HOH A:952 , HOH A:954 , HOH A:960 , FAD A:1013BINDING SITE FOR RESIDUE NAP A 1526
02AC2SOFTWAREGLY 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 , HOH A:532 , HOH A:544 , HOH A:558 , HOH A:563 , HOH A:595 , HOH A:679 , HOH A:871 , HOH A:907 , HOH A:961 , NAP A:1526 , PHE B:501BINDING SITE FOR RESIDUE FAD A 1013
03AC3SOFTWARELEU A:431 , BCT B:524 , COM B:525BINDING SITE FOR RESIDUE ACN B 1040
04AC4SOFTWAREALA 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 , BCT A:524 , HOH A:599 , CO2 A:1090 , LEU B:431BINDING SITE FOR RESIDUE KPC A 526
05AC5SOFTWARELEU A:427 , VAL A:429 , LEU A:431 , ALA A:447 , SER A:450 , HOH A:686BINDING SITE FOR RESIDUE MG A 527
06AC6SOFTWARELEU A:431 , PHE A:501 , HIS A:506 , GLN A:509 , ARG B:365 , HOH B:599 , HOH B:819 , ACN B:1040BINDING SITE FOR RESIDUE BCT B 524
07AC7SOFTWAREARG A:365 , KPC A:526 , HOH A:599 , HOH A:697 , HOH A:735 , LEU B:431 , PHE B:501 , HIS B:506 , GLN B:509BINDING SITE FOR RESIDUE BCT A 524
08AC8SOFTWAREHIS B:90 , 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 , GLU B:314 , MET B:359 , GLU B:360 , PHE B:390 , HOH B:556 , HOH B:615 , HOH B:655 , HOH B:662 , HOH B:775 , HOH B:840 , HOH B:903 , HOH B:926 , HOH B:981 , HOH B:999 , HOH B:1003 , HOH B:1006 , FAD B:1014BINDING SITE FOR RESIDUE NAP B 1526
09AC9SOFTWAREPHE A:501 , HOH A:566 , 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 , PHE B:390 , HOH B:545 , HOH B:598 , HOH B:603 , HOH B:607 , HOH B:665 , HOH B:721 , HOH B:936 , HOH B:969 , NAP B:1526BINDING SITE FOR RESIDUE FAD B 1014
10BC1SOFTWAREARG B:56 , PHE B:57 , GLY B:79 , CYS B:82 , PRO B:83 , MET B:140 , MET B:361 , ARG B:365 , ACN B:1040BINDING SITE FOR RESIDUE COM B 525
11BC2SOFTWAREPRO A:136 , KPC A:526 , HOH A:735 , ALA B:430 , LEU B:431BINDING SITE FOR RESIDUE CO2 A 1090
12BC3SOFTWARELEU B:427 , VAL B:429 , LEU B:431 , ALA B:447 , SER B:450 , HOH B:574BINDING SITE FOR RESIDUE MG B 527

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q6J)

(-) 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 3Q6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q6J)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q6J)

(-) 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 d3q6ja1 A:2-192,A:314-383 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                                                                                    d3q6ja2 A:193-313 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                      d3q6ja1 A:2-192,A:314-383                                             d3q6ja3 A:384-523 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......hhhhhhhhhhhhhhh.....eeee..........eeee..hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee....eeee..eeee..eeee...eee...eee............eehhhhhhhhh......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
                 3q6j 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 d3q6jb1 B:2-192,B:314-383 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                                                                                    d3q6jb2 B:193-313 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                      d3q6jb1 B:2-192,B:314-383                                             d3q6jb3 B:384-523 NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-3q6jB01 B:216-299                                                         ---------------------------------------------------------------------------------------Pyr_redox_dim-3q6jB05 B:387-512                                                                                               ----------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-3q6jB02 B:216-299                                                         ---------------------------------------------------------------------------------------Pyr_redox_dim-3q6jB06 B:387-512                                                                                               ----------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------Pyr_redox_2-3q6jB03 B:45-359                                                                                                                                                                                                                                                                                               -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------Pyr_redox_2-3q6jB04 B:45-359                                                                                                                                                                                                                                                                                               -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eee......hhhhhhhhhhhhhh......eeee..........eeee..hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee....eeee..eeee..eeee...eee...eee............eehhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhh..eeee..eeeeeee.....eeeeeeee..eeeeee...eee...eee.hhhhhhhhh.....................eee.hhhhh...hhhhhhhhhhhhhhhhh............eeee...eeeeee.hhhhhhhh...eeeeee.................hhhhhhh..hhhhhheeeeeee.....eeeeeeee..hhhhhhhhhhhhhh..hhhhhhhh........hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q6j 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)
  - → 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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q6J)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Pyr_redox_dim] (44)

(-) 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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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        XECC_XANP2 | Q56839: 1mo9 1mok 2c3c 2c3d

(-) Related Entries Specified in the PDB File

1mo9 NADPH DEPENDENT 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/ CARBOXYLASE COMPLEXED WITH 2-KETOPROPYLCOENZYME M
1mok NADPH DEPENDENT 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/ CARBOXYLASE
2c3d NADPH DEPENDENT 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/ CARBOXYLASE WITH A MIXED, ENZYME-COENZYME M DISULFIDE BOND