3UF0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PUTATIVE NAD(P) DEPENDENT GLUCONATE 5-DEHYDROGENASE FROM BEUTENBERGIA CAVERNAE(EFI TARGET EFI-502044) WITH BOUND NADP (LOW OCCUPANCY)

Authors :   M. W. Vetting, R. Toro, R. Bhosle, B. Hillerich, E. Washington, A. Scott S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H. J. Imker, J. A. G S. C. Almo, Enzyme Function Initiative (Efi)

Date :   31 Oct 11 (Deposition) - 23 Nov 11 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: A,B  (2x)

Keywords :   Gluconate, Gluconate 5-Dehydratase, Nad(P) Dependent, Enzyme Function Initiative, Efi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Vetting, R. Toro, R. Bhosle, B. Hillerich, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of A Putative Nad(P) Dependent Gluconate 5-Dehydrogenase From Beutenbergia Cavernae(Efi Target Efi-502044) With Bound Nadp (Low Occupancy)
To Be Published
PubMed: search

Molecule 1 - SHORT-CHAIN DEHYDROGENASE/REDUCTASE SDR
	Chains	:	A, B
	EC Number	:	1.1.1.125
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BCAV_0642
	Organism Scientific	:	BEUTENBERGIA CAVERNAE
	Organism Taxid	:	471853
	Strain	:	DSM 12333

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:16 , SER A:19 , GLY A:20 , ILE A:21 , ARG A:41 , THR A:42 , ASP A:65 , LEU A:66 , ALA A:67 , ASN A:91 , ALA A:92 , GLY A:93 , ILE A:94 , ILE A:141 , ALA A:142 , SER A:143 , TYR A:156 , LYS A:160 , PRO A:186 , GLY A:187 , TYR A:188 , VAL A:189 , THR A:191 , ASN A:193 , THR A:194 , HOH A:292 , HOH A:319 , HOH A:321 , HOH A:366 , HOH A:367	BINDING SITE FOR RESIDUE NAP A 274
2	AC2	SOFTWARE	GLY B:16 , SER B:19 , GLY B:20 , ILE B:21 , ARG B:41 , ASP B:65 , LEU B:66 , ALA B:67 , ASN B:91 , ALA B:92 , GLY B:93 , ILE B:94 , ILE B:141 , ALA B:142 , SER B:143 , TYR B:156 , LYS B:160 , PRO B:186 , GLY B:187 , VAL B:189 , THR B:191 , ALA B:192 , ASN B:193 , THR B:194 , HOH B:285 , HOH B:331 , HOH B:359	BINDING SITE FOR RESIDUE NAP B 274

(no "SS Bond" information available for 3UF0)

(no "Cis Peptide Bond" information available for 3UF0)

(no "SAP(SNP)/Variant" information available for 3UF0)

(no "PROSITE Motif" information available for 3UF0)

(no "Exon" information available for 3UF0)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:249
 aligned with C5BY10_BEUC1 | C5BY10 from UniProtKB/TrEMBL  Length:251

    Alignment length:249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242         
         C5BY10_BEUC1     3 GPFSLAGRTAVVTGAGSGIGRAIAHGYARAGAHVLAWGRTDGVKEVADEIADGGGSAEAVVADLADLEGAANVAEELAATRRVDVLVNNAGIIARAPAEEVSLGRWREVLTVNLDAAWVLSRSFGTAMLAHGSGRIVTIASMLSFQGGRNVAAYAASKHAVVGLTRALASEWAGRGVGVNALAPGYVVTANTAALRADDERAAEITARIPAGRWATPEDMVGPAVFLASDAASYVHGQVLAVDGGWLAS 251
               SCOP domains d3uf0a_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uf0 A   3 GPFSLAGRTAVVTGAGSGIGRAIAHGYARAGAHVLAWGRTDGVKEVADEIADGGGSAEAVVADLADLEGAANVAEELAATRRVDVLVNNAGIIARAPAEEVSLGRWREVLTVNLDAAWVLSRSFGTAMLAHGSGRIVTIASMLSFQGGRNVAAYAASKHAVVGLTRALASEWAGRGVGVNALAPGYVVTANTAALRADDERAAEITARIPAGRWATPEDMVGPAVFLASDAASYVHGQVLAVDGGWLAS 251
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with C5BY10_BEUC1 | C5BY10 from UniProtKB/TrEMBL  Length:251

    Alignment length:249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242         
         C5BY10_BEUC1     3 GPFSLAGRTAVVTGAGSGIGRAIAHGYARAGAHVLAWGRTDGVKEVADEIADGGGSAEAVVADLADLEGAANVAEELAATRRVDVLVNNAGIIARAPAEEVSLGRWREVLTVNLDAAWVLSRSFGTAMLAHGSGRIVTIASMLSFQGGRNVAAYAASKHAVVGLTRALASEWAGRGVGVNALAPGYVVTANTAALRADDERAAEITARIPAGRWATPEDMVGPAVFLASDAASYVHGQVLAVDGGWLAS 251
               SCOP domains d3uf0b_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uf0 B   3 GPFSLAGRTAVVTGAGSGIGRAIAHGYARAGAHVLAWGRTDGVKEVADEIADGGGSAEAVVADLADLEGAANVAEELAATRRVDVLVNNAGIIARAPAEEVSLGRWREVLTVNLDAAWVLSRSFGTAMLAHGSGRIVTIASMLSFQGGRNVAAYAASKHAVVGLTRALASEWAGRGVGVNALAPGYVVTANTAALRADDERAAEITARIPAGRWATPEDMVGPAVFLASDAASYVHGQVLAVDGGWLAS 251
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Beutenbergia cavernae [TaxId: 471853] (1)

1a	d3uf0a_	A:
1b	d3uf0b_	B:

(no "CATH Domain" information available for 3UF0)

(no "Pfam Domain" information available for 3UF0)

Asymmetric Unit(hide GO term definitions)

Chain A,B (C5BY10_BEUC1 | C5BY10)

molecular function
	GO:0008678	2-deoxy-D-gluconate 3-dehydrogenase activity	Catalysis of the reaction: 2-deoxy-D-gluconate + NAD+ = 3-dehydro-2-deoxy-D-gluconate + NADH + H+.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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: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.

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