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Title :   CRYSTAL STRUCTURE OF AN UNCHARACTERIZED SUGAR KINASE PH1459 FROM PYROCOCCUS HORIKOSHII IN COMPLEX WITH AMP-PNP

Authors :   G. Kumar, S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sg Research Center For Structural Genomics (Nysgxrc)

Date :   29 Jul 09 (Deposition) - 08 Sep 09 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Carbohydrate Kinase, Pfkb Family, Psi-Ii, 11207G, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Kumar, S. Eswaramoorthy, S. K. Burley, S. Swaminathan
Crystal Structure Of An Uncharacterized Sugar Kinase Ph1459 From Pyrococcus Horikoshii In Complex With Amp-Pnp
To Be Published
PubMed: search

Molecule 1 - UNCHARACTERIZED SUGAR KINASE PH1459
	Chains	:	A, B
	EC Number	:	2.7.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSGX3
	Expression System Strain	:	BL21(DE3) CODON + RIL
	Expression System Taxid	:	562
	Expression System Vector	:	BC PSGX3 (BC)
	Expression System Vector Type	:	PLASMID
	Gene	:	PH1459, PHCC008
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 13)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:190 , THR A:215 , GLY A:217 , GLY A:220 , TYR A:235 , VAL A:237 , PRO A:239 , ALA A:245 , GLY A:246 , ALA A:276 , HOH A:327 , HOH A:334 , HOH A:348 , HOH A:355 , HOH A:360 , HOH A:375 , HOH A:390 , HOH A:392 , HOH A:433 , HOH A:459 , HOH A:497 , HOH A:506 , HOH A:517 , HOH A:518 , HOH A:538 , ASN B:236	BINDING SITE FOR RESIDUE ANP A 900
2	AC2	SOFTWARE	PHE A:101 , LEU A:102 , LEU A:103 , ASP A:105 , ARG A:137 , ARG A:169 , HOH A:376 , HIS B:86	BINDING SITE FOR RESIDUE GOL A 901
3	AC3	SOFTWARE	HIS A:86 , PHE B:101 , LEU B:102 , LEU B:103 , ASP B:105 , ARG B:137 , LEU B:167 , ARG B:169 , HOH B:418	BINDING SITE FOR RESIDUE GOL B 901

(no "SS Bond" information available for 3IH0)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:138	-	Pro A:139
2	Asn B:138	-	Pro B:139

(no "SAP(SNP)/Variant" information available for 3IH0)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_1	PS00583	pfkB family of carbohydrate kinases signature 1.	Y1459_PYRHO	37-61	2	A:33-57 B:33-57
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	Y1459_PYRHO	245-258	2	A:241-254 B:241-254

(no "Exon" information available for 3IH0)

Asymmetric/Biological 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:304
 aligned with Y1459_PYRHO | O59128 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:304
                                    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    
          Y1459_PYRHO     6 GMIASIGELLIDLISVEEGDLKDVRLFEKHPGGAPANVAVGVSRLGVKSSLISKVGNDPFGEYLIEELSKENVDTRGIVKDEKKHTGIVFVQLKGASPSFLLYDDVAYFNMTLNDINWDIVEEAKIVNFGSVILARNPSRETVMKVIKKIKGSSLIAFDVNLRLDLWRGQEEEMIKVLEESIKLADIVKASEEEVLYLENQGVEVKGSMLTAITLGPKGCRLIKNETVVDVPSYNVNPLDTTGAGDAFMAALLVGILKLKGLDLLKLGKFANLVAALSTQKRGAWSTPRKDELLKYKEAREVLA 309
               SCOP domains d3ih0a_ A: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeee..........eeeeeeehhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeee......eeee...hhhhh.hhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhh...eeeee...hhhhhh.hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhh.......eeeee....eeeeee..eeeeee..........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PFKB_KINASES_1           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2--------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ih0 A   2 SLIASIGELLIDLISVEEGDLKDVRLFEKHPGGAPANVAVGVSRLGVKSSLISKVGNDPFGEYLIEELSKENVDTRGIVKDEKKHTGIVFVQLKGASPSFLLYDDVAYFNmTLNDINWDIVEEAKIVNFGSVILARNPSRETVmKVIKKIKGSSLIAFDVNLRLDLWRGQEEEmIKVLEESIKLADIVKASEEEVLYLENQGVEVKGSmLTAITLGPKGFRLIKNETVVDVPSYNVNPLDTTGAGDAFmAALLVGILKLKGLDLLKLGKFANLVAALSTQKRGAWSTPRKDELLKYKEAREVLA 305
                                    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    
                                                                                                                                        112-MSE                          145-MSE                       175-MSE                            210-MSE                                 250-MSE

Chain B from PDB  Type:PROTEIN  Length:304
 aligned with Y1459_PYRHO | O59128 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:304
                                    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    
          Y1459_PYRHO     6 GMIASIGELLIDLISVEEGDLKDVRLFEKHPGGAPANVAVGVSRLGVKSSLISKVGNDPFGEYLIEELSKENVDTRGIVKDEKKHTGIVFVQLKGASPSFLLYDDVAYFNMTLNDINWDIVEEAKIVNFGSVILARNPSRETVMKVIKKIKGSSLIAFDVNLRLDLWRGQEEEMIKVLEESIKLADIVKASEEEVLYLENQGVEVKGSMLTAITLGPKGCRLIKNETVVDVPSYNVNPLDTTGAGDAFMAALLVGILKLKGLDLLKLGKFANLVAALSTQKRGAWSTPRKDELLKYKEAREVLA 309
               SCOP domains d3ih0b_ B: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh.ee...eeee.....eeeeee......eeee...hhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhh...eeeee...hhhhhh.hhhhhhhhhhhhhhhh.eeeeehhhhhhhhh.........eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PFKB_KINASES_1           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2--------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ih0 B   2 SLIASIGELLIDLISVEEGDLKDVRLFEKHPGGAPANVAVGVSRLGVKSSLISKVGNDPFGEYLIEELSKENVDTRGIVKDEKKHTGIVFVQLKGASPSFLLYDDVAYFNmTLNDINWDIVEEAKIVNFGSVILARNPSRETVmKVIKKIKGSSLIAFDVNLRLDLWRGQEEEmIKVLEESIKLADIVKASEEEVLYLENQGVEVKGSmLTAITLGPKGFRLIKNETVVDVPSYNVNPLDTTGAGDAFmAALLVGILKLKGLDLLKLGKFANLVAALSTQKRGAWSTPRKDELLKYKEAREVLA 305
                                    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    
                                                                                                                                        112-MSE                          145-MSE                       175-MSE                            210-MSE                                 250-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/Biological 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)

Pyrococcus horikoshii [TaxId: 53953] (2)

1a	d3ih0a_	A:
1b	d3ih0b_	B:

(no "CATH Domain" information available for 3IH0)

(no "Pfam Domain" information available for 3IH0)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Y1459_PYRHO | O59128)

molecular function
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	GO:0004747	ribokinase activity	Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.
	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:0006014	D-ribose metabolic process	The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
	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/Biological Unit
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	Cis Peptide Bonds
		Asn A:138 - Pro A:139	[ RasMol ]
		Asn B:138 - Pro B:139	[ RasMol ]

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	Y1459_PYRHO \| O59128	:	3ewm 3gbu

3ewm	CRYSTAL STRUCTURE OF AN UNCHARACTERIZED SUGAR KINASE PH1459 FROM PYROCOCCUS HORIKOSHII
3gbu	CRYSTAL STRUCTURE OF AN UNCHARACTERIZED SUGAR KINASE PH1459 FROM PYROCOCCUS HORIKOSHII IN COMPLEX WITH ATP RELATED ID: NYSGXRC-11207G RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (7, 7)

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