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(-) Description

Title :  STRUCTURE OF RECOMBINANT CDH-H28AN484A
 
Authors :  S. Loschonsky, T. Wacker, S. Waltzer, P. P. Giovannini, M. J. Mcleish, S. L. A. Andrade, M. Mueller
Date :  04 Nov 14  (Deposition) - 21 Jan 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase, Cdh, C-C Bond Formation, C-C Bond Cleavage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Loschonsky, T. Wacker, S. Waltzer, P. P. Giovannini, M. J. Mcleish, S. L. A. Andrade, M. Muller
Extended Reaction Scope Of Thiamine Diphosphate Dependent Cyclohexane-1, 2-Dione Hydrolase: From C-C Bond Cleavage To C-C Bond Ligation.
Angew. Chem. Int. Ed. Engl. V. 53 14402 2014
PubMed-ID: 25382418  |  Reference-DOI: 10.1002/ANIE.201408287

(-) Compounds

Molecule 1 - CYCLOHEXANE-1,2-DIONE HYDROLASE
    Chains: A, B
    EC Number: 3.7.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: AZOARCUS SP.
    Organism Taxid: 62928
    Strain: BH72

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 22)

Asymmetric Unit (7, 22)
No.NameCountTypeFull Name
11PG1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
22PE2Ligand/IonNONAETHYLENE GLYCOL
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MG3Ligand/IonMAGNESIUM ION
5PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
6PG49Ligand/IonTETRAETHYLENE GLYCOL
7TPP2Ligand/IonTHIAMINE DIPHOSPHATE
Biological Unit 1 (6, 38)
No.NameCountTypeFull Name
11PG2Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
22PE4Ligand/IonNONAETHYLENE GLYCOL
3FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MG-1Ligand/IonMAGNESIUM ION
5PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
6PG418Ligand/IonTETRAETHYLENE GLYCOL
7TPP4Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS 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 , LEU A:282 , 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:2062 , HOH A:2115 , HOH A:2199 , HOH A:2200 , HOH A:2201 , HOH A:2214 , HOH A:2268BINDING SITE FOR RESIDUE FAD A1588
02AC2SOFTWAREILE 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 , MG A:1590 , HOH A:2279 , HOH A:2294 , HOH A:2356 , ILE B:26 , GLU B:52 , HIS B:76 , VAL B:78BINDING SITE FOR RESIDUE TPP A1589
03AC3SOFTWAREASP A:451 , ASN A:478 , SER A:480 , TPP A:1589 , HOH A:2279BINDING SITE FOR RESIDUE MG A1590
04AC4SOFTWAREPRO A:441 , ARG A:444 , PRO A:470 , SER A:546 , GLN A:549 , ASP A:554 , PG4 A:1594 , HOH A:2244 , HOH A:2278BINDING SITE FOR RESIDUE PG4 A1591
05AC5SOFTWARESER A:369 , GLY A:513 , ALA A:514 , LYS A:537BINDING SITE FOR RESIDUE 1PG A1592
06AC6SOFTWAREGLU A:368 , ARG A:379 , ALA A:382 , ARG A:385 , LYS A:386BINDING SITE FOR RESIDUE PG4 A1593
07AC7SOFTWAREGLN A:367 , ILE A:533 , ASP A:534 , GLY A:536 , PG4 A:1591BINDING SITE FOR RESIDUE PG4 A1594
08AC8SOFTWAREGLU A:134 , ARG A:135 , HOH A:2125 , GLU B:134 , ARG B:135 , HOH B:2056 , HOH B:2068 , HOH B:2225BINDING SITE FOR RESIDUE PG4 A1595
09AC9SOFTWAREARG A:91 , THR A:124 , PRO A:125 , ALA A:127 , ARG A:128BINDING SITE FOR RESIDUE PEG A1596
10BC1SOFTWARELYS A:66 , ARG A:218 , GLY A:220 , GLN A:494 , HOH A:2158BINDING SITE FOR RESIDUE PEG A1597
11BC2SOFTWAREGLU A:15 , HIS A:41 , GLU A:499 , MG A:1600 , HOH A:2359 , GLU B:466BINDING SITE FOR RESIDUE PG4 A1598
12BC3SOFTWAREGLN A:117 , VAL A:118 , TRP A:120 , ARG A:132 , HOH A:2071 , HOH B:2051BINDING SITE FOR RESIDUE PG4 A1599
13BC4SOFTWAREPG4 A:1598 , HOH A:2009 , HOH A:2359BINDING SITE FOR RESIDUE MG A1600
14BC5SOFTWAREHIS 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:2033 , HOH B:2063 , HOH B:2117 , HOH B:2118 , HOH B:2119 , HOH B:2129 , HOH B:2169BINDING SITE FOR RESIDUE FAD B1589
15BC6SOFTWAREILE A:26 , GLY A:27 , GLU A:52 , HIS A:76 , VAL A:78 , GLN A:116 , 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 , MG B:1591 , HOH B:2179 , HOH B:2185BINDING SITE FOR RESIDUE TPP B1590
16BC7SOFTWAREASP B:451 , ASN B:478 , SER B:480 , TPP B:1590 , HOH B:2179BINDING SITE FOR RESIDUE MG B1591
17BC8SOFTWAREVAL B:387 , ARG B:389 , PRO B:441 , ASN B:442 , SER B:443 , ARG B:444 , PRO B:470 , HOH B:2236BINDING SITE FOR RESIDUE 2PE B1592
18BC9SOFTWAREGLU B:151 , HIS B:153 , ALA B:184 , LYS B:185 , LEU B:188 , THR B:303 , PRO B:305 , PG4 B:1594 , HOH B:2237BINDING SITE FOR RESIDUE 2PE B1593
19CC1SOFTWAREARG B:148 , ARG B:183 , ALA B:184 , LEU B:308 , 2PE B:1593 , HOH B:2074BINDING SITE FOR RESIDUE PG4 B1594
20CC2SOFTWAREARG B:91 , THR B:124 , ALA B:127 , ARG B:128BINDING SITE FOR RESIDUE PG4 B1595
21CC3SOFTWAREGLN B:549BINDING SITE FOR RESIDUE PEG B1596
22CC4SOFTWAREARG A:132 , GLU A:134 , HOH A:2096 , HOH A:2101 , ALA B:109 , VAL B:118 , TRP B:120 , ARG B:132 , HOH B:2040BINDING SITE FOR RESIDUE PG4 B1597

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D5G)

(-) Cis Peptide Bonds  (7, 7)

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
5Asp B:371 -Gly B:372
6Met B:373 -Pro B:374
7Gly B:560 -Pro B:561

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D5G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D5G)

(-) Exons   (0, 0)

(no "Exon" information available for 4D5G)

(-) 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:586
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeeeee.hhhhh.........hhhhhh....eeee..hhhhhhhhhhhhhhhhh.....eeeeeeehhhhhheee..................hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eee..............eeee.....hhhhhhhhhhh.eeeee...................eeeee.hhhhh.......eeee.hhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....eeee....hhhhhhhhh.......ee.........hhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhh....eeeeee...hhhhhhhhhhhhh..........hhhhhhhhh..eeee.....hhhhhhhhhhhh...eeeeee.....................................hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d5g A   2 AIKRGADLIVEALEEYGTEQVVGFIGATSHFVADAFSKSHLGKRVINPATELGGAWMVNGYNYVKDRSAAVGAWHCVGNLLLHAAMQEARTGRIPAVHIGLNSDGRLAGRSEAAQQVPWQSFTPIARSTQRVERLDKVGEAIHEAFRVAEGHPAGPAYVDIPFDLTADQIDDKALVPRGATRAKSVLHAPNEDVREAAAQLVAAKNPVILAGGGVARSGGSEALLKLAEMVGVPVVTTSTGAGVFPETHALAMGSAGFCGWKSANDMMAAADFVLVLGSRLSDWGIAQGYITKMPKFVHVDTDPAVLGTFYFPLLSVVADAKTFMEQLIEVLPGTSGFKAVRYQERENFRQATEFRAAWDGWVREQESGDGMPASMFRAMAEVRKVQRPEDIIVTDIGNHTLPMFGGAILQRPRRLVTSMAEGILGCGFPMALGAQLAEPNSRVFLGTGDGALYYHFNEFRVAVEHKLPVITMVFTNESYGANWTLMNHQFGQNNWTEFMNPDWVGIAKAFGAYGESVRETGDIAGALQRAIDSGKPALIEIPVSKTQGLASDPVGGVGPNLLLKGREIPVDTGGSMYPGENLLHL 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      


Chain B from PDB  Type:PROTEIN  Length:587
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeeeee.hhhhh.........hhhhhh....eeee..hhhhhhhhhhhhhhhhh.....eeeeeeehhhhhheee..................hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eee..............eeee.....hhhhhhhhhhh.eeeee...................eeeee.hhhhh.......eeee.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.......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
                 4d5g B   2 AIKRGADLIVEALEEYGTEQVVGFIGATSHFVADAFSKSHLGKRVINPATELGGAWMVNGYNYVKDRSAAVGAWHCVGNLLLHAAMQEARTGRIPAVHIGLNSDGRLAGRSEAAQQVPWQSFTPIARSTQRVERLDKVGEAIHEAFRVAEGHPAGPAYVDIPFDLTADQIDDKALVPRGATRAKSVLHAPNEDVREAAAQLVAAKNPVILAGGGVARSGGSEALLKLAEMVGVPVVTTSTGAGVFPETHALAMGSAGFCGWKSANDMMAAADFVLVLGSRLSDWGIAQGYITKMPKFVHVDTDPAVLGTFYFPLLSVVADAKTFMEQLIEVLPGTSGFKAVRYQERENFRQATEFRAAWDGWVREQESGDGMPASMFRAMAEVRKVQRPEDIIVTDIGNHTLPMFGGAILQRPRRLVTSMAEGILGCGFPMALGAQLAEPNSRVFLGTGDGALYYHFNEFRVAVEHKLPVITMVFTNESYGANWTLMNHQFGQNNWTEFMNPDWVGIAKAFGAYGESVRETGDIAGALQRAIDSGKPALIEIPVSKTQGLASDPVGGVGPNLLLKGREIPVDTGGSMYPGENLLHLK 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)
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  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 4D5G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D5G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D5G)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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        CHDH_AZOSP | P0CH62: 2pgn 2pgo 4d5e

(-) Related Entries Specified in the PDB File

4d5e CRYSTAL STRUCTURE OF RECOMBINANT WILDTYPE CDH