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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE II IN COMPLEX WITH ATP AND MG+2 FROM E.COLI
 
Authors :  L. Satyanarayana, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  18 Aug 09  (Deposition) - 08 Sep 09  (Release) - 08 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Kinase, Sad, Ribose, D-Ribose Metabolic Process, Ribokinase, Pfkb Family, 11206G, Psi-Ii, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Satyanarayana, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Ribokinase (Ii)In Complex With Atp And Mg+2 From E. Coli
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE RIBOKINASE II
    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 Type: BC PSGX3 (BC)
    Fragment: FULL LENGTH
    Gene: 1040397, C4014
    Organism Scientific: ESCHERICHIA COLI O6
    Organism Taxid: 217992
    Strain: ESCHERICHIA COLI O6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric/Biological Unit (3, 21)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
3MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:448 , ATP A:900BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWARESER A:195 , LYS A:226 , ARG A:227 , GLY A:228 , GLY A:231 , TYR A:246 , VAL A:248 , GLU A:250 , THR A:254 , ALA A:256 , GLY A:257 , PHE A:260 , ASN A:282 , GLY A:285 , ALA A:286 , HOH A:334 , HOH A:358 , HOH A:366 , HOH A:373 , HOH A:376 , HOH A:400 , HOH A:429 , HOH A:435 , HOH A:443 , HOH A:448 , MG A:501BINDING SITE FOR RESIDUE ATP A 900
3AC3SOFTWAREHOH A:2 , GLU A:177 , ARG A:300 , LEU A:301 , MSE A:302 , HOH A:386BINDING SITE FOR RESIDUE MG A 502
4AC4SOFTWAREATP B:900BINDING SITE FOR RESIDUE MG B 501
5AC5SOFTWARESER B:195 , LYS B:226 , ARG B:227 , GLY B:228 , GLY B:231 , TYR B:246 , GLU B:250 , THR B:254 , ALA B:256 , GLY B:257 , PHE B:260 , ASN B:282 , GLY B:285 , HOH B:334 , HOH B:337 , HOH B:340 , HOH B:404 , HOH B:426 , MG B:501BINDING SITE FOR RESIDUE ATP B 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IQ0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:31 -Pro A:32
2Gly B:31 -Pro B:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IQ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IQ0)

(-) Exons   (0, 0)

(no "Exon" information available for 3IQ0)

(-) Sequences/Alignments

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:307
 aligned with A0A0H2VDX9_E | A0A0H2VDX9 from UniProtKB/TrEMBL  Length:320

    Alignment length:310
                                    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
         A0A0H2VDX9_E     2 SKVFTIGEILVEIMASKIGQPFDQPGIWNGPYPSGAPAIFIDQVTRLGVPCGIISCVGNDGFGDINIHRLAADGVDIRGISVLPLEATGSAFVTYHNSGDRDFIFNIKNAACGKLSAQHVDENILKDCTHFHIMGSSLFSFHMVDAVKKAVTIVKANGGVISFDPNIRKEMLDIPEMRDALHFVLELTDIYMPSEGEVLLLSPHSTPERAIAGFLEEGVKEVIVKRGNQGASYYSANEQFHVESYPVEEVDPTGAGDCFGGAWIACRQLGFDAHRALQYANACGALAVTRRGPMEGTSRLMEIETFIQRH 311
               SCOP domains d3iq0a_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeeeeee.........eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeeee..---.eeeee...hhhhhhhhhhhhhhhhh.eeeeeee.hhh.hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhh..ee..hhhhh.......hhhhhhhhhhhhh..eeeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iq0 A  -1 SKVFTIGEILVEImASKIGQPFDQPGIWNGPYPSGAPAIFIDQVTRLGVPCGIISCVGNDGFGDINIHRLAADGVDIRGISVLPLEATGSAFVTYHN---RDFIFNIKNAACGKLSAQHVDENILKDCTHFHImGSSLFSFHmVDAVKKAVTIVKANGGVISFDPNIRKEmLDIPEmRDALHFVLELTDIYmPSEGEVLLLSPHSTPERAIAGFLEEGVKEVIVKRGNQGASYYSANEQFHVESYPVEEVDPTGAGDCFGGAWIACRQLGFDAHRALQYANACGALAVTRRGPmEGTSRLmEIETFIQRH 311
                            ||      11   |    21        31        41        51        61        71        81        91      |  -|      111       121       131   |   141  |    151       161       171|     |181       191 |     201       211       221       231       241       251       261       271       281       291   |   301|      311
                            ||          15-MSE                                                                             98 102                              135-MSE  144-MSE                     172-MSE |            193-MSE                                                                                               295-MSE  |         
                           -1|                                                                                                                                                                            178-MSE                                                                                                                     302-MSE     
                             3                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:308
 aligned with A0A0H2VDX9_E | A0A0H2VDX9 from UniProtKB/TrEMBL  Length:320

    Alignment length:311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 
         A0A0H2VDX9_E     1 MSKVFTIGEILVEIMASKIGQPFDQPGIWNGPYPSGAPAIFIDQVTRLGVPCGIISCVGNDGFGDINIHRLAADGVDIRGISVLPLEATGSAFVTYHNSGDRDFIFNIKNAACGKLSAQHVDENILKDCTHFHIMGSSLFSFHMVDAVKKAVTIVKANGGVISFDPNIRKEMLDIPEMRDALHFVLELTDIYMPSEGEVLLLSPHSTPERAIAGFLEEGVKEVIVKRGNQGASYYSANEQFHVESYPVEEVDPTGAGDCFGGAWIACRQLGFDAHRALQYANACGALAVTRRGPMEGTSRLMEIETFIQRH 311
               SCOP domains d3iq0b_ B: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeee............eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeee..---....eeee....hhhhh............eeeeeee.hhh.hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhh..ee..hhhhh.......hhhhhhhhhhhhh..eeeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iq0 B  -2 LSKVFTIGEILVEImASKIGQPFDQPGIWNGPYPSGAPAIFIDQVTRLGVPCGIISCVGNDGFGDINIHRLAADGVDIRGISVLPLEATGSAFVTY---GDRDFIFNIKNAACGKLSAQHVDENILKDCTHFHImGSSLFSFHmVDAVKKAVTIVKANGGVISFDPNIRKEmLDIPEmRDALHFVLELTDIYmPSEGEVLLLSPHSTPERAIAGFLEEGVKEVIVKRGNQGASYYSANEQFHVESYPVEEVDPTGAGDCFGGAWIACRQLGFDAHRALQYANACGALAVTRRGPmEGTSRLmEIETFIQRH 311
                             ||     10    |   20        30        40        50        60        70        80        90     | 100       110       120       130    |  140   |   150       160       170 |     180       190  |    200       210       220       230       240       250       260       270       280       290    |  300 |     310 
                            -1|          15-MSE                                                                           96 100                                135-MSE  144-MSE                     172-MSE |            193-MSE                                                                                               295-MSE  |         
                              3                                                                                                                                                                            178-MSE                                                                                                                     302-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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IQ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IQ0)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3IQ0)

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 Related Entries

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UniProtKB/TrEMBL
        A0A0H2VDX9_E | A0A0H2VDX9: 3k9e

(-) Related Entries Specified in the PDB File

3h49 CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE (APO FORM) FROM E.COLI AT 1.8A RESOLUTION
3hic THE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE(LIN2199)FROM LISTERIA INNOCUA
3i3y CRYSTAL STRUCTURE OF RIBOKINASE IN COMPLEX WITH D-RIBOSE FROM KLEBSIELLA PNEUMONIAE
3ie7 THE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE (LIN2199) FROM LISTERIA INNOCUA IN COMPLEX WITH ATP AT 1.6A RELATED ID: NYSGXRC-11206G RELATED DB: TARGETDB
3ikh CRYSTAL STRUCTURE OF RIBOKINASE IN COMPLEX WITH ATP AND GLYCEROL IN THE ACTIVE SITE FROM KLEBSIELLA PNEUMONIAE
3in1 CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE IN COMPLEX WITH ADP FROM E.COLI