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Title :   THE CRYSTAL STRUCTURE OF FAD AND THDP-DEPENDENT CYCLOHEXANE-1,2-DIONE HYDROLASE IN COMPLEX WITH CYCLOHEXANE-1,2-DIONE

Authors :   S. Fraas, E. Warkentin, U. Ermler

Date :   10 Apr 07 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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 :   S. Fraas, A. K. Steinbach, E. Warkentin, P. M. H. Kroneck, U. Ermler
The Crystal Structure Of Fad And Thdp-Dependent Cyclohexane-1, 2-Dione Hydrolase In Complex With Cyclohexane-1, 2-Dione
To Be Published
PubMed: search

Molecule 1 - CYCLOHEXANE-1,2-DIONE HYDROLASE (CDH)
	Chains	:	A, B
	Organism Scientific	:	AZOARCUS SP.
	Strain	:	22LIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 17)

No.	Name	Count	Type	Full Name
1	CXO	2	Ligand/Ion	CYCLOHEXANE-1,2-DIONE
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	P6G	9	Ligand/Ion	HEXAETHYLENE GLYCOL
5	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (4, 30)

No.	Name	Count	Type	Full Name
1	CXO	4	Ligand/Ion	CYCLOHEXANE-1,2-DIONE
2	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	P6G	18	Ligand/Ion	HEXAETHYLENE GLYCOL
5	TPP	4	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:451 , ASN A:478 , SER A:480 , HOH A:1768	BINDING SITE FOR RESIDUE MG A 610
02	AC2	SOFTWARE	ASP B:451 , ASN B:478 , SER B:480 , HOH B:845	BINDING SITE FOR RESIDUE MG B 611
03	AC3	SOFTWARE	LYS A:185 , LEU A:188 , THR A:303 , PRO A:305 , HOH A:1919	BINDING SITE FOR RESIDUE P6G A 646
04	AC4	SOFTWARE	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 , 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:1604 , HOH A:1625 , HOH A:1637 , HOH A:1638 , HOH A:1649 , HOH A:1759 , HOH A:1764	BINDING SITE FOR RESIDUE FAD A 612
05	AC5	SOFTWARE	HIS 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 , SER B:283 , TRP B:285 , GLY B:286 , ASP B:302 , THR B:303 , ASP B:304 , ASP B:321 , ALA B:322 , PHE B:406 , SER B:420 , MET B:421 , ALA B:422 , GLY B:424 , HOH B:650 , HOH B:655 , HOH B:673 , HOH B:699 , HOH B:719 , HOH B:837 , HOH B:840	BINDING SITE FOR RESIDUE FAD B 613
06	AC6	SOFTWARE	ILE 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:1670 , HOH A:1768 , ILE B:26 , GLU B:52 , HIS B:76	BINDING SITE FOR RESIDUE TPP A 614
07	AC7	SOFTWARE	ILE A:26 , GLU A:52 , HIS A:76 , 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:708 , HOH B:845	BINDING SITE FOR RESIDUE TPP B 615
08	AC8	SOFTWARE	TRP A:285 , ASN A:484 , GLY B:27 , HIS B:28 , HIS B:76 , GLN B:116	BINDING SITE FOR RESIDUE CXO B 601
09	AC9	SOFTWARE	GLY A:27 , HIS A:28 , HIS A:76 , GLN A:116 , TRP B:285 , ASN B:484	BINDING SITE FOR RESIDUE CXO A 1601
10	BC1	SOFTWARE	TRP A:120 , ARG A:132 , HOH A:1700 , HOH A:1923 , HOH B:854	BINDING SITE FOR RESIDUE P6G A 641
11	BC2	SOFTWARE	ARG B:91 , THR B:124 , PRO B:125 , ALA B:127 , ARG B:128 , HOH B:964 , HOH B:1049	BINDING SITE FOR RESIDUE P6G B 642
12	BC3	SOFTWARE	HOH A:1776 , TRP B:120 , ARG B:132 , HOH B:789 , HOH B:1122 , HOH B:1158	BINDING SITE FOR RESIDUE P6G B 643
13	BC4	SOFTWARE	LYS A:510 , ALA A:511 , ASP B:504	BINDING SITE FOR RESIDUE P6G A 644
14	BC5	SOFTWARE	ARG A:91 , THR A:124 , PRO A:125 , ARG A:128 , HOH A:1948	BINDING SITE FOR RESIDUE P6G A 645
15	BC6	SOFTWARE	GLU A:466 , HOH A:1760 , GLU B:16 , HIS B:41 , GLU B:499 , MET B:501	BINDING SITE FOR RESIDUE P6G A 647
16	BC7	SOFTWARE	ARG B:389 , PRO B:441 , SER B:443 , ARG B:444 , HOH B:997 , HOH B:1113	BINDING SITE FOR RESIDUE P6G B 648
17	BC8	SOFTWARE	TRP B:363 , GLU B:366 , GLN B:367 , ILE B:533 , ASP B:534 , GLY B:536 , SER B:546 , ASP B:554 , HOH B:929 , HOH B:997 , HOH B:1251	BINDING SITE FOR RESIDUE P6G B 649

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

Asymmetric Unit

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

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

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

(no "Exon" information available for 2PGN)

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.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeeeee.hhhhh.........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
                 2pgn 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.hhhhhhhhhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeeeee.hhhhh.........hhhhhh....eeee..hhhhhhhhhhhhhhhhh.....eeeeeeehhhhhheee..................hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eee..............eeee.....hhhhhhhhhhh.eeeee...................eeeee.hhhhh.......eeee.hhhhhhhhhhhhhhhh......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
                 2pgn 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 '\|'

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

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CHDH_AZOSP | P0CH62)


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.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		CXO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:560 - Pro A:561	[ RasMol ]
		Gly B:560 - Pro B:561	[ RasMol ]
		His A:153 - Pro A:154	[ RasMol ]
		His B:153 - Pro B:154	[ RasMol ]
		Met A:373 - Pro A:374	[ RasMol ]
		Met B:373 - Pro B:374	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2pgn
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	CHDH_AZOSP \| P0CH62	:	2pgo 4d5e 4d5g

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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