3PL2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A 5-KETO-2-DEOXYGLUCONOKINASE (NCGL0155, CGL0158) FROM CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO AT 1.89 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   12 Nov 10 (Deposition) - 24 Nov 10 (Release) - 20 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

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

Keywords :   Pfkb Pfam Motif, Inositol Phosphate Metabolism, Ribokinase-Like Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A 5-Keto-2-Deoxygluconokinase (Ncgl0155, Cgl0158) From Corynebacterium Glutamicum Atcc 13032 Kitasato At 1. 89 A Resolution
To Be Published
PubMed: search

Molecule 1 - SUGAR KINASE, RIBOKINASE FAMILY
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEQUENCE DATABASE RESIDUES 22-339
	Gene	:	IOLC, CGL0158, CG0197
	Organism Scientific	:	CORYNEBACTERIUM GLUTAMICUM
	Organism Taxid	:	1718
	Synonym	:	SUGAR KINASES, RIBOKINASE FAMILY, 5-KETO-2- DEOXYGLUCONOKINASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 17)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 8)

No.	Name	Count	Type	Full Name
1	CIT	-1	Ligand/Ion	CITRIC ACID
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:15 , GLY B:41 , SER B:42 , ASN B:45 , PHE B:111 , ARG B:174 , LEU B:260 , GLY B:261 , ASP B:264 , HOH B:492 , HOH B:621 , HOH B:856 , HOH B:919 , HOH B:938	BINDING SITE FOR RESIDUE CIT B 400

(no "SS Bond" information available for 3PL2)

Asymmetric Unit

No.	Residues
1	Pro A:103	-	Pro A:104
2	Glu A:114	-	Pro A:115
3	Glu A:148	-	Pro A:149
4	Arg A:165	-	His A:166
5	Pro B:103	-	Pro B:104
6	Glu B:114	-	Pro B:115
7	Glu B:148	-	Pro B:149
8	Arg B:165	-	His B:166
9	Pro C:103	-	Pro C:104
10	Glu C:114	-	Pro C:115
11	Glu C:148	-	Pro C:149
12	Arg C:165	-	His C:166
13	Pro D:103	-	Pro D:104
14	Glu D:114	-	Pro D:115
15	Glu D:148	-	Pro D:149
16	Arg D:165	-	His D:166

(no "SAP(SNP)/Variant" information available for 3PL2)

(no "PROSITE Motif" information available for 3PL2)

(no "Exon" information available for 3PL2)

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:310
 aligned with Q8NTZ3_CORGL | Q8NTZ3 from UniProtKB/TrEMBL  Length:339

    Alignment length:310
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336
         Q8NTZ3_CORGL    27 STHEVLAIGRLGVDIYPLQSGVGLADVQSFGKYLGGSAANVSVAAARHGHNSALLSRVGNDPFGEYLLAELERLGVDNQYVATDQTFKTPVTFCEIFPPDDFPLYFYREPKAPDLNIESADVSLDDVREADILWFTLTGFSEEPSRGTHREILTTRANRRHTIFDLDYRPMFWESPEEATKQAEWALQHSTVAVGNKEECEIAVGETEPERAGRALLERGVELAIVKQGPKGVMAMTKDETVEVPPFFVDVINGLGAGDAFGGALCHGLLSEWPLEKVLRFANTAGALVASRLECSTAMPTTDEVEASLN 336
               SCOP domains d3pl2a_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeee.......hhhhh.....eeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh.ee...eeee......eeee.........eeee....hhhhhhhhhhhhhhhhhhh.eeeee.hhhh..hhhhhhhhhhhhhh....eeee...hhhhh.hhhhhhhhhhhhhh...eeeehhhhhhhhhh..hhhhhhhhhhhh...eeeeeee..eeeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pl2 A   6 STHEVLAIGRLGVDIYPLQSGVGLADVQSFGKYLGGSAANVSVAAARHGHNSALLSRVGNDPFGEYLLAELERLGVDNQYVATDQTFKTPVTFCEIFPPDDFPLYFYREPKAPDLNIESADVSLDDVREADILWFTLTGFSEEPSRGTHREILTTRANRRHTIFDLDYRPmFWESPEEATKQAEWALQHSTVAVGNKEECEIAVGETEPERAGRALLERGVELAIVKQGPKGVmAmTKDETVEVPPFFVDVINGLGAGDAFGGALCHGLLSEWPLEKVLRFANTAGALVASRLECSTAmPTTDEVEASLN 315
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175|      185       195       205       215       225       235   | | 245       255       265       275       285       295       305       315
                                                                                                                                                                                                    176-MSE                                                        239-MSE                                                          304-MSE       
                                                                                                                                                                                                                                                                     241-MSE

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with Q8NTZ3_CORGL | Q8NTZ3 from UniProtKB/TrEMBL  Length:339

    Alignment length:310
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336
         Q8NTZ3_CORGL    27 STHEVLAIGRLGVDIYPLQSGVGLADVQSFGKYLGGSAANVSVAAARHGHNSALLSRVGNDPFGEYLLAELERLGVDNQYVATDQTFKTPVTFCEIFPPDDFPLYFYREPKAPDLNIESADVSLDDVREADILWFTLTGFSEEPSRGTHREILTTRANRRHTIFDLDYRPMFWESPEEATKQAEWALQHSTVAVGNKEECEIAVGETEPERAGRALLERGVELAIVKQGPKGVMAMTKDETVEVPPFFVDVINGLGAGDAFGGALCHGLLSEWPLEKVLRFANTAGALVASRLECSTAMPTTDEVEASLN 336
               SCOP domains d3pl2b_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeee.......hhhhh.....eeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee......eeee.........eeee....hhhhhhhhhhhhhhhhhhh.eeeee.hhhh..hhhhhhhhhhhhhh....eeee...hhhhh.hhhhhhhhhhhhhh...eeeeehhhhhhhhh..hhhhhhhhhhhhh..eeeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pl2 B   6 STHEVLAIGRLGVDIYPLQSGVGLADVQSFGKYLGGSAANVSVAAARHGHNSALLSRVGNDPFGEYLLAELERLGVDNQYVATDQTFKTPVTFCEIFPPDDFPLYFYREPKAPDLNIESADVSLDDVREADILWFTLTGFSEEPSRGTHREILTTRANRRHTIFDLDYRPmFWESPEEATKQAEWALQHSTVAVGNKEECEIAVGETEPERAGRALLERGVELAIVKQGPKGVmAmTKDETVEVPPFFVDVINGLGAGDAFGGALCHGLLSEWPLEKVLRFANTAGALVASRLECSTAmPTTDEVEASLN 315
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175|      185       195       205       215       225       235   | | 245       255       265       275       285       295       305       315
                                                                                                                                                                                                    176-MSE                                                        239-MSE                                                          304-MSE       
                                                                                                                                                                                                                                                                     241-MSE

Chain C from PDB  Type:PROTEIN  Length:310
 aligned with Q8NTZ3_CORGL | Q8NTZ3 from UniProtKB/TrEMBL  Length:339

    Alignment length:310
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336
         Q8NTZ3_CORGL    27 STHEVLAIGRLGVDIYPLQSGVGLADVQSFGKYLGGSAANVSVAAARHGHNSALLSRVGNDPFGEYLLAELERLGVDNQYVATDQTFKTPVTFCEIFPPDDFPLYFYREPKAPDLNIESADVSLDDVREADILWFTLTGFSEEPSRGTHREILTTRANRRHTIFDLDYRPMFWESPEEATKQAEWALQHSTVAVGNKEECEIAVGETEPERAGRALLERGVELAIVKQGPKGVMAMTKDETVEVPPFFVDVINGLGAGDAFGGALCHGLLSEWPLEKVLRFANTAGALVASRLECSTAMPTTDEVEASLN 336
               SCOP domains d3pl2c_ C: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeeeee.....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh.ee...eeee......eeee.........eeee....hhhhhhhhhhhhhhhhhhh.eeeee.hhhh..hhhhhhhhhhhhhh....eeee...hhhhh.hhhhhhhhhhhhhhh..eeeehhhhhhhhhh..hhhhhhhhhhhh...eeeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pl2 C   6 STHEVLAIGRLGVDIYPLQSGVGLADVQSFGKYLGGSAANVSVAAARHGHNSALLSRVGNDPFGEYLLAELERLGVDNQYVATDQTFKTPVTFCEIFPPDDFPLYFYREPKAPDLNIESADVSLDDVREADILWFTLTGFSEEPSRGTHREILTTRANRRHTIFDLDYRPmFWESPEEATKQAEWALQHSTVAVGNKEECEIAVGETEPERAGRALLERGVELAIVKQGPKGVmAmTKDETVEVPPFFVDVINGLGAGDAFGGALCHGLLSEWPLEKVLRFANTAGALVASRLECSTAmPTTDEVEASLN 315
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175|      185       195       205       215       225       235   | | 245       255       265       275       285       295       305       315
                                                                                                                                                                                                    176-MSE                                                        239-MSE                                                          304-MSE       
                                                                                                                                                                                                                                                                     241-MSE

Chain D from PDB  Type:PROTEIN  Length:309
 aligned with Q8NTZ3_CORGL | Q8NTZ3 from UniProtKB/TrEMBL  Length:339

    Alignment length:309
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326         
         Q8NTZ3_CORGL    27 STHEVLAIGRLGVDIYPLQSGVGLADVQSFGKYLGGSAANVSVAAARHGHNSALLSRVGNDPFGEYLLAELERLGVDNQYVATDQTFKTPVTFCEIFPPDDFPLYFYREPKAPDLNIESADVSLDDVREADILWFTLTGFSEEPSRGTHREILTTRANRRHTIFDLDYRPMFWESPEEATKQAEWALQHSTVAVGNKEECEIAVGETEPERAGRALLERGVELAIVKQGPKGVMAMTKDETVEVPPFFVDVINGLGAGDAFGGALCHGLLSEWPLEKVLRFANTAGALVASRLECSTAMPTTDEVEASL 335
               SCOP domains d3pl2d_ D: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -PfkB-3pl2D01 D:7-307                                                                                                                                                                                                                                                                                         ------- Pfam domains (1)
           Pfam domains (2) -PfkB-3pl2D02 D:7-307                                                                                                                                                                                                                                                                                         ------- Pfam domains (2)
           Pfam domains (3) -PfkB-3pl2D03 D:7-307                                                                                                                                                                                                                                                                                         ------- Pfam domains (3)
           Pfam domains (4) -PfkB-3pl2D04 D:7-307                                                                                                                                                                                                                                                                                         ------- Pfam domains (4)
         Sec.struct. author ....eeee...eeeeee...........eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee......eeee.........eeee....hhhhhhhhhhhhhhhhhhh.eeeee.hhhh..hhhhhhhhhhhhhh....eeee...hhhhh.hhhhhhhhhhhhhh...eeeeehhhhhhhhh..hhhhhhhhhhhh...eeeeeee..eeeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pl2 D   6 STHEVLAIGRLGVDIYPLQSGVGLADVQSFGKYLGGSAANVSVAAARHGHNSALLSRVGNDPFGEYLLAELERLGVDNQYVATDQTFKTPVTFCEIFPPDDFPLYFYREPKAPDLNIESADVSLDDVREADILWFTLTGFSEEPSRGTHREILTTRANRRHTIFDLDYRPmFWESPEEATKQAEWALQHSTVAVGNKEECEIAVGETEPERAGRALLERGVELAIVKQGPKGVmAmTKDETVEVPPFFVDVINGLGAGDAFGGALCHGLLSEWPLEKVLRFANTAGALVASRLECSTAmPTTDEVEASL 314
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175|      185       195       205       215       225       235   | | 245       255       265       275       285       295       305         
                                                                                                                                                                                                    176-MSE                                                        239-MSE                                                          304-MSE      
                                                                                                                                                                                                                                                                     241-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: Alpha and beta proteins (a/b) (23833)

Fold: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: automated matches (88)

Protein domain: automated matches (88)

Corynebacterium glutamicum [TaxId: 1718] (1)

1a	d3pl2a_	A:
1b	d3pl2b_	B:
1c	d3pl2c_	C:
1d	d3pl2d_	D:

(no "CATH Domain" information available for 3PL2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ribokinase (55)

Family: PfkB (39)

Corynebacterium glutamicum (Brevibacterium flavum) (1)

1a	PfkB-3pl2D01	D:7-307
1b	PfkB-3pl2D02	D:7-307
1c	PfkB-3pl2D03	D:7-307
1d	PfkB-3pl2D04	D:7-307

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q8NTZ3_CORGL | Q8NTZ3)

molecular function
	GO:0008865	fructokinase activity	Catalysis of the reaction: ATP + D-fructose = ADP + D-fructose 6-phosphate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0046835	carbohydrate phosphorylation	The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Arg A:165 - His A:166	[ RasMol ]
		Arg B:165 - His B:166	[ RasMol ]
		Arg C:165 - His C:166	[ RasMol ]
		Arg D:165 - His D:166	[ RasMol ]
		Glu A:114 - Pro A:115	[ RasMol ]
		Glu A:148 - Pro A:149	[ RasMol ]
		Glu B:114 - Pro B:115	[ RasMol ]
		Glu B:148 - Pro B:149	[ RasMol ]
		Glu C:114 - Pro C:115	[ RasMol ]
		Glu C:148 - Pro C:149	[ RasMol ]
		Glu D:114 - Pro D:115	[ RasMol ]
		Glu D:148 - Pro D:149	[ RasMol ]
		Pro A:103 - Pro A:104	[ RasMol ]
		Pro B:103 - Pro B:104	[ RasMol ]
		Pro C:103 - Pro C:104	[ RasMol ]
		Pro D:103 - Pro D:104	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 17)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (16, 16)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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