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(-) Description

Title :  THE CRYSTAL STRUCTURE OF FAD AND THDP DEPENDENT CYCLOHEXANE-1,2-DIONE HYDROLASE (CDH) FROM AZOARCUS SP. STRAIN 22LIN
 
Authors :  A. K. Steinbach, E. Warkentin, P. M. H. Kroneck, U. Ermler
Date :  10 Apr 07  (Deposition) - 22 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.26
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Three Alpha/Beta Domains, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Steinbach, J. Harder, E. Warkentin, P. M. H. Kroneck, U. Ermler
The Crystal Structure Of Fad And Thdp Dependent Cyclohexane-1, 2-Dione Hydrolase (Cdh) From Azoarcus Sp. Strain 22Lin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYCLOHEXANE-1,2-DIONE HYDROLASE (CDH)
    ChainsA, B
    Organism ScientificAZOARCUS SP.
    Strain22LIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 11)

Asymmetric Unit (6, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MG2Ligand/IonMAGNESIUM ION
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5PO41Ligand/IonPHOSPHATE ION
6TPP2Ligand/IonTHIAMINE DIPHOSPHATE
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MG-1Ligand/IonMAGNESIUM ION
4MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5PO42Ligand/IonPHOSPHATE ION
6TPP4Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN B:388 , ILE B:410 , GLN B:412BINDING SITE FOR RESIDUE PO4 B 625
02AC2SOFTWAREASP A:451 , ASN A:478 , SER A:480 , HOH A:711BINDING SITE FOR RESIDUE MG A 608
03AC3SOFTWAREHIS B:28 , HIS B:76 , GLN B:116BINDING SITE FOR RESIDUE CL B 610
04AC4SOFTWAREASP B:451 , ASN B:478 , SER B:480 , HOH B:721BINDING SITE FOR RESIDUE MG B 609
05AC5SOFTWAREHIS A:28 , HIS A:76 , GLN A:116BINDING SITE FOR RESIDUE CL A 611
06AC6SOFTWAREARG A:94 , HIS A:153 , GLY A:213 , GLY A:214 , GLY A:215 , ARG A:218 , SER A:219 , THR A:239 , SER A:240 , THR A:241 , ALA A:257 , GLY A:258 , PHE A:259 , CYS A:260 , GLY A:261 , GLY A:279 , SER A:280 , ARG A:281 , SER A:283 , TRP A:285 , GLY A:286 , ASP A:302 , THR A:303 , ASP A:304 , ALA A:320 , ASP A:321 , ALA A:322 , SER A:420 , MET A:421 , ALA A:422 , GLY A:424 , HOH A:644 , HOH A:657 , HOH A:664 , HOH A:686 , HOH A:687 , HOH A:818 , HOH A:819BINDING SITE FOR RESIDUE FAD A 612
07AC7SOFTWAREILE A:398 , GLY A:399 , ASN A:400 , HIS A:401 , GLY A:424 , LEU A:426 , GLY A:450 , ASP A:451 , GLY A:452 , ALA A:453 , TYR A:456 , ASN A:478 , SER A:480 , TYR A:481 , GLY A:482 , ALA A:483 , ASN A:484 , HOH A:692 , HOH A:711 , ILE B:26 , GLU B:52 , HIS B:76BINDING SITE FOR RESIDUE TPP A 614
08AC8SOFTWAREHIS B:153 , GLY B:213 , GLY B:214 , GLY B:215 , ARG B:218 , SER B:219 , THR B:239 , SER B:240 , THR B:241 , ALA B:257 , GLY B:258 , PHE B:259 , CYS B:260 , GLY B:261 , GLY B:279 , SER B:280 , ARG B:281 , LEU B:282 , SER B:283 , TRP B:285 , GLY B:286 , ASP B:302 , THR B:303 , ASP B:304 , ALA B:320 , ASP B:321 , ALA B:322 , SER B:420 , MET B:421 , ALA B:422 , GLY B:424 , HOH B:633 , HOH B:647 , HOH B:656 , HOH B:677 , HOH B:727 , HOH B:857 , HOH B:896BINDING SITE FOR RESIDUE FAD B 613
09AC9SOFTWAREILE A:26 , GLU A:52 , HIS A:76 , HOH A:1148 , ILE B:398 , GLY B:399 , ASN B:400 , HIS B:401 , GLY B:424 , LEU B:426 , GLY B:450 , ASP B:451 , GLY B:452 , ALA B:453 , TYR B:456 , ASN B:478 , SER B:480 , TYR B:481 , GLY B:482 , ALA B:483 , ASN B:484 , HOH B:645 , HOH B:721BINDING SITE FOR RESIDUE TPP B 615
10BC1SOFTWAREGLY A:399 , LEU A:487 , LEU A:551 , LEU A:563 , HOH A:696 , HIS B:28BINDING SITE FOR RESIDUE MPD A 620
11BC2SOFTWARETHR A:249 , GLN A:388 , ILE A:410 , GLN A:412BINDING SITE FOR RESIDUE MPD A 621

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1His A:153 -Pro A:154
2Met A:373 -Pro A:374
3Gly A:560 -Pro A:561
4His B:153 -Pro B:154
5Met B:373 -Pro B:374
6Gly B:560 -Pro B:561

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PGO)

(-) 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:587
 aligned with CHDH_AZOSP | P0CH62 from UniProtKB/Swiss-Prot  Length:589

    Alignment length:587
                                    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       531       541       551       561       571       581       
           CHDH_AZOSP     2 AIKRGADLIVEALEEYGTEQVVGFIGHTSHFVADAFSKSHLGKRVINPATELGGAWMVNGYNYVKDRSAAVGAWHCVGNLLLHAAMQEARTGRIPAVHIGLNSDGRLAGRSEAAQQVPWQSFTPIARSTQRVERLDKVGEAIHEAFRVAEGHPAGPAYVDIPFDLTADQIDDKALVPRGATRAKSVLHAPNEDVREAAAQLVAAKNPVILAGGGVARSGGSEALLKLAEMVGVPVVTTSTGAGVFPETHALAMGSAGFCGWKSANDMMAAADFVLVLGSRLSDWGIAQGYITKMPKFVHVDTDPAVLGTFYFPLLSVVADAKTFMEQLIEVLPGTSGFKAVRYQERENFRQATEFRAAWDGWVREQESGDGMPASMFRAMAEVRKVQRPEDIIVTDIGNHTLPMFGGAILQRPRRLVTSMAEGILGCGFPMALGAQLAEPNSRVFLGTGDGALYYHFNEFRVAVEHKLPVITMVFTNESYGANWTLMNHQFGQNNWTEFMNPDWVGIAKAFGAYGESVRETGDIAGALQRAIDSGKPALIEIPVSKTQGLASDPVGGVGPNLLLKGREIPVDTGGSMYPGENLLHLK 588
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeeeee...............hhhhhh....eeee..hhhhhhhhhhhhhhhhh.....eeeeeeehhhhhheee..................hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eee..............eeee.....hhhhhhhhhhh.eeeee...................eeeee.hhhhh.......eeee.hhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.....eeee....hhhhhhhhh.......ee.........hhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhh....eeeeee...hhhhhhhhhhhhh..........hhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeeeee....................................hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pgo A   2 AIKRGADLIVEALEEYGTEQVVGFIGHTSHFVADAFSKSHLGKRVINPATELGGAWMVNGYNYVKDRSAAVGAWHCVGNLLLHAAMQEARTGRIPAVHIGLNSDGRLAGRSEAAQQVPWQSFTPIARSTQRVERLDKVGEAIHEAFRVAEGHPAGPAYVDIPFDLTADQIDDKALVPRGATRAKSVLHAPNEDVREAAAQLVAAKNPVILAGGGVARSGGSEALLKLAEMVGVPVVTTSTGAGVFPETHALAMGSAGFCGWKSANDMMAAADFVLVLGSRLSDWGIAQGYITKMPKFVHVDTDPAVLGTFYFPLLSVVADAKTFMEQLIEVLPGTSGFKAVRYQERENFRQATEFRAAWDGWVREQESGDGMPASMFRAMAEVRKVQRPEDIIVTDIGNHTLPMFGGAILQRPRRLVTSMAEGILGCGFPMALGAQLAEPNSRVFLGTGDGALYYHFNEFRVAVEHKLPVITMVFTNESYGANWTLMNHQFGQNNWTEFMNPDWVGIAKAFGAYGESVRETGDIAGALQRAIDSGKPALIEIPVSKTQGLASDPVGGVGPNLLLKGREIPVDTGGSMYPGENLLHLK 588
                                    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       531       541       551       561       571       581       

Chain B from PDB  Type:PROTEIN  Length:587
 aligned with CHDH_AZOSP | P0CH62 from UniProtKB/Swiss-Prot  Length:589

    Alignment length:587
                                    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       531       541       551       561       571       581       
           CHDH_AZOSP     2 AIKRGADLIVEALEEYGTEQVVGFIGHTSHFVADAFSKSHLGKRVINPATELGGAWMVNGYNYVKDRSAAVGAWHCVGNLLLHAAMQEARTGRIPAVHIGLNSDGRLAGRSEAAQQVPWQSFTPIARSTQRVERLDKVGEAIHEAFRVAEGHPAGPAYVDIPFDLTADQIDDKALVPRGATRAKSVLHAPNEDVREAAAQLVAAKNPVILAGGGVARSGGSEALLKLAEMVGVPVVTTSTGAGVFPETHALAMGSAGFCGWKSANDMMAAADFVLVLGSRLSDWGIAQGYITKMPKFVHVDTDPAVLGTFYFPLLSVVADAKTFMEQLIEVLPGTSGFKAVRYQERENFRQATEFRAAWDGWVREQESGDGMPASMFRAMAEVRKVQRPEDIIVTDIGNHTLPMFGGAILQRPRRLVTSMAEGILGCGFPMALGAQLAEPNSRVFLGTGDGALYYHFNEFRVAVEHKLPVITMVFTNESYGANWTLMNHQFGQNNWTEFMNPDWVGIAKAFGAYGESVRETGDIAGALQRAIDSGKPALIEIPVSKTQGLASDPVGGVGPNLLLKGREIPVDTGGSMYPGENLLHLK 588
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeeeee...............hhhhhh....eeee..hhhhhhhhhhhhhhhhh.....eeeeeeehhhhhheee..................hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eee..............eeee.....hhhhhhhhhhh.eeeee...................eeeee.hhhhh.......eeee.hhhhhhhhhhhhh.........hhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.....eeee....hhhhhhhhh.......ee.........hhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhh....eeeeee...hhhhhhhhhhhhh..........hhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeeeee....................................hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pgo B   2 AIKRGADLIVEALEEYGTEQVVGFIGHTSHFVADAFSKSHLGKRVINPATELGGAWMVNGYNYVKDRSAAVGAWHCVGNLLLHAAMQEARTGRIPAVHIGLNSDGRLAGRSEAAQQVPWQSFTPIARSTQRVERLDKVGEAIHEAFRVAEGHPAGPAYVDIPFDLTADQIDDKALVPRGATRAKSVLHAPNEDVREAAAQLVAAKNPVILAGGGVARSGGSEALLKLAEMVGVPVVTTSTGAGVFPETHALAMGSAGFCGWKSANDMMAAADFVLVLGSRLSDWGIAQGYITKMPKFVHVDTDPAVLGTFYFPLLSVVADAKTFMEQLIEVLPGTSGFKAVRYQERENFRQATEFRAAWDGWVREQESGDGMPASMFRAMAEVRKVQRPEDIIVTDIGNHTLPMFGGAILQRPRRLVTSMAEGILGCGFPMALGAQLAEPNSRVFLGTGDGALYYHFNEFRVAVEHKLPVITMVFTNESYGANWTLMNHQFGQNNWTEFMNPDWVGIAKAFGAYGESVRETGDIAGALQRAIDSGKPALIEIPVSKTQGLASDPVGGVGPNLLLKGREIPVDTGGSMYPGENLLHLK 588
                                    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       531       541       551       561       571       581       

   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  (0, 0)

(no "SCOP Domain" information available for 2PGO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PGO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CHDH_AZOSP | P0CH62)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.

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 Related Entries

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

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        CHDH_AZOSP | P0CH622pgn 4d5e 4d5g

(-) Related Entries Specified in the PDB File

2pgn