1MZR - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF DKGA FROM E.COLI AT 2.13 A RESOLUTION SOLVED BY MOLECULAR REPLACEMENT

Authors :   C. Abergel, S. Jeudy, V. Monchois, J. M. Claverie, Bacterial Targets Cnrs, France (Bigs)

Date :   09 Oct 02 (Deposition) - 28 Oct 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.13

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

Keywords :   Alpha/Beta-Barrel, Aldo-Ketoreductase, Nadph Dependant, Bacterial Targets At Igs-Cnrs, France, Bigs, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Jeudy, V. Monchois, C. Maza, J. M. Claverie, C. Abergel
Crystal Structure Of Escherichia Coli Dkga, A Broad-Specificity Aldo-Keto Reductase.
Proteins V. 62 302 2006
PubMed-ID: 16284956 | Reference-DOI: 10.1002/PROT.20710

Molecule 1 - 2,5-DIKETO-D-GLUCONATE REDUCTASE A
	Chains	:	A, B
	EC Number	:	1.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PDEST17
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	YQHE
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PO4	5	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:188 , PRO A:189 , LEU A:190 , PRO A:231 , LYS A:232 , HOH A:667 , HOH A:677	BINDING SITE FOR RESIDUE PO4 A 900
2	AC2	SOFTWARE	SER A:233 , VAL A:234 , THR A:235 , ARG A:238	BINDING SITE FOR RESIDUE PO4 A 901
3	AC3	SOFTWARE	SER B:188 , PRO B:189 , LEU B:190 , ALA B:191 , PRO B:231 , LYS B:232 , HOH B:639 , HOH B:770	BINDING SITE FOR RESIDUE PO4 B 902
4	AC4	SOFTWARE	ARG A:171 , GLN A:172 , ASP A:262 , HOH A:363 , ARG B:171 , GLN B:172 , ASP B:262 , HOH B:316 , HOH B:398	BINDING SITE FOR RESIDUE PO4 B 904
5	AC5	SOFTWARE	LYS B:84 , ARG B:85 , PRO B:86 , ARG B:87 , HOH B:325 , HOH B:412 , HOH B:476	BINDING SITE FOR RESIDUE PO4 B 905
6	AC6	SOFTWARE	TRP A:24 , TYR A:52 , TRP A:79 , HIS A:108 , TRP A:109 , HOH A:497 , GOL A:911	BINDING SITE FOR RESIDUE GOL A 910
7	AC7	SOFTWARE	GLN A:25 , TRP A:79 , GOL A:910	BINDING SITE FOR RESIDUE GOL A 911

(no "SS Bond" information available for 1MZR)

(no "Cis Peptide Bond" information available for 1MZR)

(no "SAP(SNP)/Variant" information available for 1MZR)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	DKGA_ECOLI	41-58	2	A:42-59 B:42-59
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	DKGA_ECOLI	123-140	2	A:124-141 B:124-141
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	DKGA_ECOLI	229-244	2	A:230-245 B:230-245

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	DKGA_ECOLI	41-58	1	A:42-59 -
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	DKGA_ECOLI	123-140	1	A:124-141 -
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	DKGA_ECOLI	229-244	1	A:230-245 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	DKGA_ECOLI	41-58	1	- B:42-59
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	DKGA_ECOLI	123-140	1	- B:124-141
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	DKGA_ECOLI	229-244	1	- B:230-245

(no "Exon" information available for 1MZR)

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:274
 aligned with DKGA_ECOLI | Q46857 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:274
                                    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    
           DKGA_ECOLI     2 ANPTVIKLQDGNVMPQLGLGVWQASNEEVITAIQKALEVGYRSIDTAAAYKNEEGVGKALKNASVNREELFITTKLWNDDHKRPREALLDSLKKLQLDYIDLYLMHWPVPAIDHYVEAWKGMIELQKEGLIKSIGVCNFQIHHLQRLIDETGVTPVINQIELHPLMQQRQLHAWNATHKIQTESWSPLAQGGKGVFDQKVIRDLADKYGKTPAQIVIRWHLDSGLVVIPKSVTPSRIAENFDVWDFRLDKDELGEIAKLDQGKRLGPDPDQFGG 275
               SCOP domains d1mzra_ A: 2,5-diketo-D-gluconic acid reductase A                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1mzrA00 A:3-276 NADP-dependent oxidoreductase                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.....eee...ee....hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh..hhhhheeeeeehhhhh.hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh....eeeee......hhhhhhhhhhh..eeeee............hhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhh........hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mzr A   3 ANPTVIKLQDGNVMPQLGLGVWQASNEEVITAIQKALEVGYRSIDTAAAYKNEEGVGKALKNASVNREELFITTKLWNDDHKRPREALLDSLKKLQLDYIDLYLMHWPVPAIDHYVEAWKGMIELQKEGLIKSIGVCNFQIHHLQRLIDETGVTPVINQIELHPLMQQRQLHAWNATHKIQTESWSPLAQGGKGVFDQKVIRDLADKYGKTPAQIVIRWHLDSGLVVIPKSVTPSRIAENFDVWDFRLDKDELGEIAKLDQGKRLGPDPDQFGG 276
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with DKGA_ECOLI | Q46857 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:276
                             1                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269      
           DKGA_ECOLI     - -MANPTVIKLQDGNVMPQLGLGVWQASNEEVITAIQKALEVGYRSIDTAAAYKNEEGVGKALKNASVNREELFITTKLWNDDHKRPREALLDSLKKLQLDYIDLYLMHWPVPAIDHYVEAWKGMIELQKEGLIKSIGVCNFQIHHLQRLIDETGVTPVINQIELHPLMQQRQLHAWNATHKIQTESWSPLAQGGKGVFDQKVIRDLADKYGKTPAQIVIRWHLDSGLVVIPKSVTPSRIAENFDVWDFRLDKDELGEIAKLDQGKRLGPDPDQFGG 275
               SCOP domains d1mzrb_ B: 2,5-diketo-D-gluconic acid reductase A                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1mzrB00 B:1-276 NADP-dependent oxidoreductase                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) -----------------Aldo_ket_red-1mzrB01 B:18-263                                                                                                                                                                                                                         ------------- Pfam domains (1)
           Pfam domains (2) -----------------Aldo_ket_red-1mzrB02 B:18-263                                                                                                                                                                                                                         ------------- Pfam domains (2)
         Sec.struct. author ......eee.....eee...ee....hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh..hhhhheeeeeehhhhh.hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh....eeeee......hhhhhhhhhhh..eeeee............hhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mzr B   1 GLANPTVIKLQDGNVMPQLGLGVWQASNEEVITAIQKALEVGYRSIDTAAAYKNEEGVGKALKNASVNREELFITTKLWNDDHKRPREALLDSLKKLQLDYIDLYLMHWPVPAIDHYVEAWKGMIELQKEGLIKSIGVCNFQIHHLQRLIDETGVTPVINQIELHPLMQQRQLHAWNATHKIQTESWSPLAQGGKGVFDQKVIRDLADKYGKTPAQIVIRWHLDSGLVVIPKSVTPSRIAENFDVWDFRLDKDELGEIAKLDQGKRLGPDPDQFGG 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: NAD(P)-linked oxidoreductase (286)

Family: Aldo-keto reductases (NADP) (251)

Protein domain: 2,5-diketo-D-gluconic acid reductase A (5)

Escherichia coli [TaxId: 562] (1)

1a	d1mzra_	A:
1b	d1mzrb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: NADP-dependent oxidoreductase (181)

Escherichia coli. Organism_taxid: 562. (2)

1a	1mzrB00	B:1-276
1b	1mzrA00	A:3-276

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Aldo_ket_red] (94)

Family: Aldo_ket_red (94)

Escherichia coli (strain K12) (4)

1a	Aldo_ket_red-1mzrB01	B:18-263
1b	Aldo_ket_red-1mzrB02	B:18-263

Asymmetric Unit(hide GO term definitions)

Chain A,B (DKGA_ECOLI | Q46857)

molecular function
	GO:0050580	2,5-didehydrogluconate reductase activity	Catalysis of the reaction: 2-dehydro-D-gluconate + NADP+ = 2,5-didehydro-D-gluconate + NADPH + H+.
	GO:0008106	alcohol dehydrogenase (NADP+) activity	Catalysis of the reaction: an alcohol + NADP+ = an aldehyde + NADPH + H+.
	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.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0019853	L-ascorbic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions.
	GO:0051596	methylglyoxal catabolic process	The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, the aldehyde of pyruvic acid.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	Cis Peptide Bonds
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Biological Units
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	1mzr
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	1.1.1.-
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

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