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Title :   THE CRYSTAL STRUCTURE OF ADENOSINE KINASE FROM SINORHIZOBIUM MELILOTI

Authors :   Z. Zhang, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich, A. Kar, J R. Seidel, G. Villigas, W. Zencheck, S. C. Almo, S. Swaminathan, New Y Structural Genomics Research Consortium (Nysgrc)

Date :   24 Oct 11 (Deposition) - 09 Nov 11 (Release) - 09 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Adenosine Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhang, S. C. Almo, S. Swaminathan
The Crystal Structure Of Adenosine Kinase From Sinorhizobiu Meliloti
To Be Published
PubMed: search

Molecule 1 - ADENOSINE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	R00171, SMC02846
	Organism Common	:	ENSIFER MELILOTI
	Organism Scientific	:	SINORHIZOBIUM MELILOTI
	Organism Taxid	:	382

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 16)

No.	Name	Count	Type	Full Name
1	ADN	2	Ligand/Ion	ADENOSINE
2	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:11 , ILE A:13 , ASP A:15 , MSE A:35 , GLY A:58 , GLY A:59 , SER A:60 , ASN A:63 , MSE A:127 , THR A:129 , GLU A:156 , TYR A:158 , GLY A:275 , ASP A:278 , PRO A:314	BINDING SITE FOR RESIDUE ADN A 353
2	AC2	SOFTWARE	ASN A:215 , THR A:245 , LEU A:246 , SER A:247 , GLU A:248 , GLY A:250 , SER A:265 , LEU A:267 , ALA A:276 , GLY A:277 , ASN A:302 , ALA A:305 , ILE A:309	BINDING SITE FOR RESIDUE ADP A 354
3	AC3	SOFTWARE	ASN B:11 , ILE B:13 , ASP B:15 , MSE B:35 , GLY B:58 , GLY B:59 , SER B:60 , ASN B:63 , MSE B:127 , THR B:129 , GLU B:156 , TYR B:158 , GLY B:275 , ASP B:278 , PRO B:314	BINDING SITE FOR RESIDUE ADN B 353
4	AC4	SOFTWARE	ASN B:215 , THR B:245 , LEU B:246 , SER B:247 , GLU B:248 , GLY B:250 , ALA B:264 , SER B:265 , LEU B:267 , ALA B:276 , GLY B:277 , TYR B:280 , ASN B:302 , ALA B:305 , ILE B:309 , HOH B:371 , HOH B:374	BINDING SITE FOR RESIDUE ADP B 354

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

Asymmetric/Biological Unit

No.	Residues
1	His A:109	-	Pro A:110
2	His B:109	-	Pro B:110

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

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

(no "Exon" information available for 3UBO)

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:338
 aligned with Q92T17_RHIME | Q92T17 from UniProtKB/TrEMBL  Length:330

    Alignment length:338
                                                                                                                                                                                                                                                                                                                                                                  330         
                                    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       311       321        |-        
         Q92T17_RHIME     2 AKYDVLTIGNAIVDIIARCDDSFLEENGIIKGAMNLINADRAELLYSRMGPAVEASGGSAGNTAAGVASLGGRAAYFGKVADDQLGEIFTHDIRAQGVHFQTKPLDGHPPTARSMIFVTEDGERSMNTYLGACVELGPEDVEDDVVAQSKVTYFEGYLWDPPRAKDAIREAARIAHAHGRETAMTLSDSFCVHRYRSEFLELMRSGTVDIVFANRQEALALYETEDFDRALELLARDCKLAAVTLSEEGSVVVRGAERVRVGASVLEQVVDTTGAGDLYAAGFLFGYTSGRSLEECSKLGNLAAGIVIGQIGPRPLVSLATAARQAALV---------   -
               SCOP domains d3uboa_ A: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee.hhhhhhhh......eee.hhhhhhhhhhh....eeee.hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh................eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhheeeeeee.hhh....hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhh....eeeeehhhhhhhh...hhhhhhhhhhhhh....eehhhhheeeee..eeeee............hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ubo A   2 AKYDVLTIGNAIVDIIARCDDSFLEENGIIKGAmNLINADRAELLYSRmGPAVEASGGSAGNTAAGVASLGGRAAYFGKVADDQLGEIFTHDIRAQGVHFQTKPLDGHPPTARSmIFVTEDGERSmNTYLGACVELGPEDVEDDVVAQSKVTYFEGYLWDPPRAKDAIREAARIAHAHGRETAmTLSDSFCVHRYRSEFLELmRSGTVDIVFANRQEALALYETEDFDRALELLARDCKLAAVTLSEEGSVVVRGAERVRVGASVLEQVVDTTGAGDLYAAGFLFGYTSGRSLEECSKLGNLAAGIVIGQIGPRPLVSLATAARQAALVAENLYFQSH 339
                                    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       311       321       331        
                                                            35-MSE         50-MSE                                                           116-MSE    127-MSE                                                   185-MSE            204-MSE

Chain B from PDB  Type:PROTEIN  Length:327
 aligned with Q92T17_RHIME | Q92T17 from UniProtKB/TrEMBL  Length:330

    Alignment length:327
                                    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       311       321       
         Q92T17_RHIME     2 AKYDVLTIGNAIVDIIARCDDSFLEENGIIKGAMNLINADRAELLYSRMGPAVEASGGSAGNTAAGVASLGGRAAYFGKVADDQLGEIFTHDIRAQGVHFQTKPLDGHPPTARSMIFVTEDGERSMNTYLGACVELGPEDVEDDVVAQSKVTYFEGYLWDPPRAKDAIREAARIAHAHGRETAMTLSDSFCVHRYRSEFLELMRSGTVDIVFANRQEALALYETEDFDRALELLARDCKLAAVTLSEEGSVVVRGAERVRVGASVLEQVVDTTGAGDLYAAGFLFGYTSGRSLEECSKLGNLAAGIVIGQIGPRPLVSLATAARQAA 328
               SCOP domains d3ubob_ B: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee.hhhhhhhh......eee.hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh................eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhheeeeeee.hhhh..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhh....eeeeehhhhhhh....hhhhhhhhhhhhh.eeeee.hhh.eeeee..eeeee............hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ubo B   2 AKYDVLTIGNAIVDIIARCDDSFLEENGIIKGAmNLINADRAELLYSRmGPAVEASGGSAGNTAAGVASLGGRAAYFGKVADDQLGEIFTHDIRAQGVHFQTKPLDGHPPTARSmIFVTEDGERSmNTYLGACVELGPEDVEDDVVAQSKVTYFEGYLWDPPRAKDAIREAARIAHAHGRETAmTLSDSFCVHRYRSEFLELmRSGTVDIVFANRQEALALYETEDFDRALELLARDCKLAAVTLSEEGSVVVRGAERVRVGASVLEQVVDTTGAGDLYAAGFLFGYTSGRSLEECSKLGNLAAGIVIGQIGPRPLVSLATAARQAA 328
                                    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       311       321       
                                                            35-MSE         50-MSE                                                           116-MSE    127-MSE                                                   185-MSE            204-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)

Rhizobium meliloti (Sinorhizobium meliloti) [TaxId: 382] (1)

1a	d3uboa_	A:
1b	d3ubob_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q92T17_RHIME | Q92T17)

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: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: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: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/Biological Unit
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	Cis Peptide Bonds
		His A:109 - Pro A:110	[ RasMol ]
		His B:109 - Pro B:110	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 16)

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Cis Peptide Bonds (2, 2)

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