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(-) Description

Title :  STRUCTURAL GENOMICS, THE CRYSTAL STRUCTURE OF A PUTATIVE KINASE FROM SALMONELLA TYPHIMURIM LT2
 
Authors :  R. Zhang, M. Zhou, D. Holzle, F. Collart, A. Joachimiak, Midwest Cente Structural Genomics (Mcsg)
Date :  10 Aug 05  (Deposition) - 27 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Structural Genomics, Putative Kinase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, M. Zhou, D. Holzle, F. Collart, A. Joachimiak
The Crystal Structure Of A Putative Kinase From Salmonella Typhimurim Lt2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE KINASE
    Chains: A, B, C, D
    EC Number: 2.7.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YFJB
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AN1)

(-) Sites  (0, 0)

(no "Site" information available for 2AN1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AN1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AN1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AN1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AN1)

(-) Exons   (0, 0)

(no "Exon" information available for 2AN1)

(-) Sequences/Alignments

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:275
 aligned with NADK_SALTY | P65774 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:289
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
           NADK_SALTY     4 HFKCIGIVGHPRHPTALTTHEMLYRWLCDQGYEVIVEQQIAHELQLKNVPTGTLAEIGQQADLAVVVGGDGNMLGAARTLARYDINVIGINRGNLGFLTDLDPDNALQQLSDVLEGRYISEKRFLLEAQVCQQDRQKRISTAINEVVLHPGKVAHMIEFEVYIDETFAFSQRSDGLIISTPTGSTAYSLSAGGPILTPSLDAITLVPMFPHTLSARPLVINSSSTIRLRFSHRRSDLEISCDSQIALPIQEGEDVLIRRCDYHLNLIHPKDYSYFNTLSTKLGWSKKLF 292
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2an1A01 A:       4-127,A:265-292 Probable inorganic polyphosphate/atp-NAD kinase; domain 1                                  2an1A02 A    :128-264 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                          2an1A01 A:4-127,A:265-292    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..-------hhhhhhhhhhhhh..eeeeehhhhhhh......eehhhhhhhhh.eeee..hhhhhhhhhhhhh....eeee...............hhhhhhhhhhh..eeeeeeeeeeeeee..----.eeee..eeeeee......eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh...ee.....eeeeeee.........eeee....eeeee..---.eeeee.....eee....eeeeeeeeeeeeeeee...hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2an1 A   4 HFKCIGIVGH-------TTHEMLYRWLCDQGYEVIVEQQIAHELQLKNVPTGTLAEIGQQADLAVVVGGDGNMLGAARTLARYDINVIGINRGNLGFLTDLDPDNALQQLSDVLEGRYISEKRFLLEAQVCQQ----RISTAINEVVLHPGKVAHMIEFEVYIDETFAFSQRSDGLIISTPTGSTAYSLSAGGPILTPSLDAITLVPMFPHTLSARPLVINSSSTIRLRFSH---DLEISCDSQIALPIQEGEDVLIRRCDYHLNLIHPKDYSYFNTLSTKLGWSKKLF 292
                                    13       |23        33        43        53        63        73        83        93       103       113       123       133  |    143       153       163       173       183       193       203       213       223       233 |   | 243       253       263       273       283         
                                    13      21                                                                                                                136  141                                                                                           235 239                                                     


Chain B from PDB  Type:PROTEIN  Length:281
 aligned with NADK_SALTY | P65774 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:289
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
           NADK_SALTY     4 HFKCIGIVGHPRHPTALTTHEMLYRWLCDQGYEVIVEQQIAHELQLKNVPTGTLAEIGQQADLAVVVGGDGNMLGAARTLARYDINVIGINRGNLGFLTDLDPDNALQQLSDVLEGRYISEKRFLLEAQVCQQDRQKRISTAINEVVLHPGKVAHMIEFEVYIDETFAFSQRSDGLIISTPTGSTAYSLSAGGPILTPSLDAITLVPMFPHTLSARPLVINSSSTIRLRFSHRRSDLEISCDSQIALPIQEGEDVLIRRCDYHLNLIHPKDYSYFNTLSTKLGWSKKLF 292
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2an1B01 B:       4-127,B:265-292 Probable inor ganic polyphosphate/atp-NAD kinase; domain 1                                 2an1B02 B:128-264 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                              2an1B01 B:4-127,B:265-292    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..-------hhhhhhhhhhhhh..eeeeehhhhhh...-...eehhhhhhhhh.eeee..hhhhhhhhhhhhh....eeee...............hhhhhhhhhhh..eeeeeeeeeeeeeee..eeeeeeee..eeeeee......eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh...ee.....eeeeeee.........eeee....eeeeeee....eeeee...eeee.....eeeeeeeeeeeeeeee...hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2an1 B   4 HFKCIGIVGH-------TTHEMLYRWLCDQGYEVIVEQQIAHELQL-NVPTGTLAEIGQQADLAVVVGGDGNMLGAARTLARYDINVIGINRGNLGFLTDLDPDNALQQLSDVLEGRYISEKRFLLEAQVCQQDRQKRISTAINEVVLHPGKVAHMIEFEVYIDETFAFSQRSDGLIISTPTGSTAYSLSAGGPILTPSLDAITLVPMFPHTLSARPLVINSSSTIRLRFSHRRSDLEISCDSQIALPIQEGEDVLIRRCDYHLNLIHPKDYSYFNTLSTKLGWSKKLF 292
                                    13       |23        33        43     | |53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
                                    13      21                          49 |                                                                                                                                                                                                                                                 
                                                                          51                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:271
 aligned with NADK_SALTY | P65774 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:286
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      
           NADK_SALTY     5 FKCIGIVGHPRHPTALTTHEMLYRWLCDQGYEVIVEQQIAHELQLKNVPTGTLAEIGQQADLAVVVGGDGNMLGAARTLARYDINVIGINRGNLGFLTDLDPDNALQQLSDVLEGRYISEKRFLLEAQVCQQDRQKRISTAINEVVLHPGKVAHMIEFEVYIDETFAFSQRSDGLIISTPTGSTAYSLSAGGPILTPSLDAITLVPMFPHTLSARPLVINSSSTIRLRFSHRRSDLEISCDSQIALPIQEGEDVLIRRCDYHLNLIHPKDYSYFNTLSTKLGWSKK 290
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2an1C01 C       :5-127,C:265-290 Probable in   organic polyphosphate/atp-NAD kinase; domain 1                              2an1C02 C:128-264 Probable i  norganic polyphosphate/atp-NAD kinase; domain 2                                                            2an1C01 C:5-127,C:265-290  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..-------hhhhhhhhhhhhh..eeeeehhhhh...---..eehhhhhhhhh.eeeeehhhhhhhhhhhhhh....eeeee..............hhhhhhhhhhh..eeeeeeeeeeeeeee..eeeeeeee..eeeee...--..eeeeeee..eeeeeeee.eeeee..hhhhhhhhhh...ee.....eeeeeee.........eeee....eeee..---..eeeee.....eee....eeeeeeeeeeeeeeee...hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2an1 C   5 FKCIGIVGH-------TTHEMLYRWLCDQGYEVIVEQQIAHELQ---VPTGTLAEIGQQADLAVVVGGDGNMLGAARTLARYDINVIGINRGNLGFLTDLDPDNALQQLSDVLEGRYISEKRFLLEAQVCQQDRQKRISTAINEVVLHPGK--HMIEFEVYIDETFAFSQRSDGLIISTPTGSTAYSLSAGGPILTPSLDAITLVPMFPHTLSARPLVINSSSTIRLRFS---SDLEISCDSQIALPIQEGEDVLIRRCDYHLNLIHPKDYSYFNTLSTKLGWSKK 290
                                    |-      | 24        34        44   |   |54        64        74        84        94       104       114       124       134       144       154|  |   164       174       184       194       204       214       224       234   |   244       254       264       274       284      
                                   13      21                         48  52                                                                                                    155  |                                                                         234 238                                                    
                                                                                                                                                                                   158                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:268
 aligned with NADK_SALTY | P65774 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:289
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
           NADK_SALTY     4 HFKCIGIVGHPRHPTALTTHEMLYRWLCDQGYEVIVEQQIAHELQLKNVPTGTLAEIGQQADLAVVVGGDGNMLGAARTLARYDINVIGINRGNLGFLTDLDPDNALQQLSDVLEGRYISEKRFLLEAQVCQQDRQKRISTAINEVVLHPGKVAHMIEFEVYIDETFAFSQRSDGLIISTPTGSTAYSLSAGGPILTPSLDAITLVPMFPHTLSARPLVINSSSTIRLRFSHRRSDLEISCDSQIALPIQEGEDVLIRRCDYHLNLIHPKDYSYFNTLSTKLGWSKKLF 292
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2an1D01 D         :4-127,D:265-292 Pr         o bable inorganic polyphosphate/atp-NAD kinase; domain 1                      2an1D02 D:128-264 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                              2an1D01 D:4-127,D:265-292    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.---------hhhhhhhhhhhh..eeee.---------.-....hhhhhhhhh.eeeeehhhhhhhhhhhhhh....eeeee..............hhhhhhhhhhh..eee..eeeeeeeeee..eeeeeeee..eeeeee......eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh...ee.....eeeeeee.........eeee....eeeee...--.eeeee.....eee....eeeeeeeeeeeeeeee...hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2an1 D   4 HFKCIGIVG---------THEMLYRWLCDQGYEVIVE---------K-VPTGTLAEIGQQADLAVVVGGDGNMLGAARTLARYDINVIGINRGNLGFLTDLDPDNALQQLSDVLEGRYISEKRFLLEAQVCQQDRQKRISTAINEVVLHPGKVAHMIEFEVYIDETFAFSQRSDGLIISTPTGSTAYSLSAGGPILTPSLDAITLVPMFPHTLSARPLVINSSSTIRLRFSHR--DLEISCDSQIALPIQEGEDVLIRRCDYHLNLIHPKDYSYFNTLSTKLGWSKKLF 292
                                    |-        23        33      |  -      | 53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233  |  | 243       253       263       273       283         
                                   12        22                40        50 |                                                                                                                                                                                     236  |                                                     
                                                                           52                                                                                                                                                                                        239
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2AN1)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AN1)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (NADK_SALTY | P65774)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0003951    NAD+ kinase activity    Catalysis of the reaction: ATP + NAD(+) = ADP + 2 H(+) + NADP(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0019674    NAD metabolic process    The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
    GO:0006741    NADP biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; biosynthesis may be of either the oxidized form, NADP, or the reduced form, NADPH.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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