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Title :   CRYSTAL STRUCTURE OF 5-KETO-4-DEOXYURONATE ISOMERASE FROM ESCHERICIA COLI

Authors :   R. L. Crowther, M. M. Georgiadis

Date :   15 Oct 04 (Deposition) - 05 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

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

Keywords :   Beta Barrel, Cupin, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. L. Crowther, M. M. Georgiadis
The Crystal Structure Of 5-Keto-4-Deoxyuronate Isomerase From Escherichia Coli
Proteins V. 61 680 2005
PubMed-ID: 16152643 | Reference-DOI: 10.1002/PROT.20598

Molecule 1 - 4-DEOXY-L-THREO-5-HEXOSULOSE-URONATE KETOL-ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	KDUI
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	5-KETO-4-DEOXYURONATE ISOMERASE, DKI ISOMERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 26)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 72)

No.	Name	Count	Type	Full Name
1	1PE	6	Ligand/Ion	PENTAETHYLENE GLYCOL
2	MSE	66	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:196 , HIS A:198 , GLU A:203 , HIS A:245	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	HIS B:196 , HIS B:198 , GLU B:203 , HIS B:245	BINDING SITE FOR RESIDUE ZN B 502
3	AC3	SOFTWARE	ILE A:163 , LYS A:165 , VAL A:168 , TRP A:257 , PHE A:266 , HOH A:712	BINDING SITE FOR RESIDUE 1PE A 503
4	AC4	SOFTWARE	ILE B:163 , LYS B:165 , VAL B:168 , TRP B:257 , PHE B:266 , HOH B:682 , HOH B:738	BINDING SITE FOR RESIDUE 1PE B 504

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

Asymmetric Unit

No.	Residues
1	Mse A:193	-	Pro A:194
2	Mse B:193	-	Pro B:194

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

(no "PROSITE Motif" information available for 1XRU)

(no "Exon" information available for 1XRU)

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:281
 aligned with KDUI_ECOLI | Q46938 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:281
                               1                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277 
           KDUI_ECOLI     - ---MDVRQSIHSAHAKTLDTQGLRNEFLVEKVFVADEYTMVYSHIDRIIVGGIMPITKTVSVGGEVGKQLGVSYFLERRELGVINIGGAGTITVDGQCYEIGHRDALYVGKGAKEVVFASIDTGTPAKFYYNCAPAHTTYPTKKVTPDEVSPVTLGDNLTSNRRTINKYFVPDVLETCQLSMGLTELAPGNLWNTMPCHTHERRMEVYFYFNMDDDACVFHMMGQPQETRHIVMHNEQAVISPSWSIHSGVGTKAYTFIWGMVGENQVFDDMDHVAVKDLR 278
               SCOP domains ---d1xrua1 A:1-277 5-keto-4-deoxyuronate isomerase KduI                                                                                                                                                                                                                                 - SCOP domains
               CATH domains 1xruA01   1xruA02               1xruA01 A:-2-7,A:30-143 pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1                        1xruA02 A:8-29,A:144-278 4-deoxy-l-threo-5-hexosulose-uronate ketol- isomerase; domain 2                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhhh..hhhhhhhhhee...........eee....eeeeee......eeehhhhhhhh........eeeeeee....eeeee..eeeee....eeee......eeeee........eeeeeee.......eeehhhhhh.eee.hhhhh..eeeeeee..........eeeeeee.....ee...eee...eeeeeeee.......eeeeeee..eeeeeee...eeeee....eeeeee....eeeeeeee........eeehhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xru A  -2 GSAMDVRQSIHSAHAKTLDTQGLRNEFLVEKVFVADEYTmVYSHIDRIIVGGImPITKTVSVGGEVGKQLGVSYFLERRELGVINIGGAGTITVDGQCYEIGHRDALYVGKGAKEVVFASIDTGTPAKFYYNCAPAHTTYPTKKVTPDEVSPVTLGDNLTSNRRTINKYFVPDVLETCQLSmGLTELAPGNLWNTmPCHTHERRmEVYFYFNmDDDACVFHmmGQPQETRHIVmHNEQAVISPSWSIHSGVGTKAYTFIWGmVGENQVFDDmDHVAVKEIC 278
                                     7        17        27        37        47   |    57        67        77        87        97       107       117       127       137       147       157       167       177 |     187     | 197    |  207  |    217 ||    227   |   237       247       257 |     267 |     277 
                                                                  37-MSE        51-MSE                                                                                                                         179-MSE       193-MSE  202-MSE 210-MSE  219-MSE     231-MSE                     259-MSE   269-MSE     
                                                                                                                                                                                                                                                        220-MSE

Chain B from PDB  Type:PROTEIN  Length:281
 aligned with KDUI_ECOLI | Q46938 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:281
                               1                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277 
           KDUI_ECOLI     - ---MDVRQSIHSAHAKTLDTQGLRNEFLVEKVFVADEYTMVYSHIDRIIVGGIMPITKTVSVGGEVGKQLGVSYFLERRELGVINIGGAGTITVDGQCYEIGHRDALYVGKGAKEVVFASIDTGTPAKFYYNCAPAHTTYPTKKVTPDEVSPVTLGDNLTSNRRTINKYFVPDVLETCQLSMGLTELAPGNLWNTMPCHTHERRMEVYFYFNMDDDACVFHMMGQPQETRHIVMHNEQAVISPSWSIHSGVGTKAYTFIWGMVGENQVFDDMDHVAVKDLR 278
               SCOP domains d1xrub_ B: 5-keto-4-deoxyuronate isomerase KduI                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1xruB01   1xruB02               1xruB01 B:-2-7,B:30-143 pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1                        1xruB02 B:8-29,B:144-278 4-deoxy-l-threo-5-hexosulose-uronate ketol- isomerase; domain 2                                                CATH domains
           Pfam domains (1) --------------------------KduI-1xruB01 B:24-274                                                                                                                                                                                                                                      ---- Pfam domains (1)
           Pfam domains (2) --------------------------KduI-1xruB02 B:24-274                                                                                                                                                                                                                                      ---- Pfam domains (2)
         Sec.struct. author ....eee...hhhhhh..hhhhhhhhhee...........eee....eeeeee......eeehhhhhhhh........eeeeeee....eeeee..eeeee....eeee......eeeee........eeeeeee.......eeehhhhh..eee.hhhhh..eeeeeee..........eeeeeee..........eee...eeeeeeee.......eeeeeee..eeeeeee...eeeee....eeeeee....eeeeeeee........eeehhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xru B  -2 GSAMDVRQSIHSAHAKTLDTQGLRNEFLVEKVFVADEYTmVYSHIDRIIVGGImPITKTVSVGGEVGKQLGVSYFLERRELGVINIGGAGTITVDGQCYEIGHRDALYVGKGAKEVVFASIDTGTPAKFYYNCAPAHTTYPTKKVTPDEVSPVTLGDNLTSNRRTINKYFVPDVLETCQLSmGLTELAPGNLWNTmPCHTHERRmEVYFYFNmDDDACVFHmmGQPQETRHIVmHNEQAVISPSWSIHSGVGTKAYTFIWGmVGENQVFDDmDHVAVKEIC 278
                                     7        17        27        37        47   |    57        67        77        87        97       107       117       127       137       147       157       167       177 |     187     | 197    |  207  |    217 ||    227   |   237       247       257 |     267 |     277 
                                                                  37-MSE        51-MSE                                                                                                                         179-MSE       193-MSE  202-MSE 210-MSE  219-MSE     231-MSE                     259-MSE   269-MSE     
                                                                                                                                                                                                                                                        220-MSE

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: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: RmlC-like cupins (220)

Family: KduI-like (3)

Protein domain: 5-keto-4-deoxyuronate isomerase KduI (3)

Escherichia coli [TaxId: 562] (2)

1a	d1xrua1	A:1-277
1b	d1xrub_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: 4-deoxy-l-threo-5-hexosulose-uronate ketol- isomerase; domain 2 (2)

Escherichia coli. Organism_taxid: 562. (2)

1a	1xruA02	A:8-29,A:144-278
1b	1xruB02	B:8-29,B:144-278

Homologous Superfamily: pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1 (2)

Escherichia coli. Organism_taxid: 562. (2)

2a	1xruA01	A:-2-7,A:30-143
2b	1xruB01	B:-2-7,B:30-143

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: KduI (2)

Escherichia coli (strain K12) (1)

1a	KduI-1xruB01	B:24-274
1b	KduI-1xruB02	B:24-274

Asymmetric Unit(hide GO term definitions)

Chain A,B (KDUI_ECOLI | Q46938)

molecular function
	GO:0008697	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity	Catalysis of the reaction: 5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016861	intramolecular oxidoreductase activity, interconverting aldoses and ketoses	Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor, which is an aldose or a ketose, are the same molecule, and no oxidized product appears.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0019698	D-galacturonate catabolic process	The chemical reactions and pathways resulting in the breakdown of D-galacturonate, the D-enantiomer of galacturonate, the anion of galacturonic acid.
	GO:0042840	D-glucuronate catabolic process	The chemical reactions and pathways resulting in the breakdown of D-glucuronate, the D-enantiomer of glucuronate.
	GO:0045490	pectin catabolic process	The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
		Mse A:193 - Pro A:194	[ RasMol ]
		Mse B:193 - Pro B:194	[ RasMol ]

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	1xru
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(no "Related Entries Specified in the PDB File" available for 1XRU)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 26)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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