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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOKINASE IN COMPLEX WITH ATP AND GLYCEROL IN THE ACTIVE SITE FROM KLEBSIELLA PNEUMONIAE
 
Authors :  L. Satyanarayana, S. K. Burley, S. Swaminathan, New York Sgx Resear For Structural Genomics (Nysgxrc)
Date :  05 Aug 09  (Deposition) - 18 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Transferase, Kinase, Sad, Ribose, D-Ribose Metabolic Process, Atp, Ribokinase, Pfkb Family, 11206L1, Psi-Ii, Nysgxrc, Structural Genomics, , Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Satyanarayana, S. K. Burley, S. Swaminathan
Crystal Structure Of Ribokinase In Complex With Atp And Glycerol In The Active Site From Klebsiella Pneumoniae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CARBOHYDRATE KINASE
    ChainsA, B, C, D
    EC Number2.7.1.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPSGX3 (BC)
    Expression System StrainBL21(DE3) CODON + RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneKPN78578_16990, KPN78578_16990/5340552, KPN_01729
    Organism ScientificKLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE MGH 78578
    Organism Taxid272620
    StrainATCC700721/MGH78578)

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric Unit (3, 26)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:182 , THR A:200 , GLY A:202 , GLY A:205 , VAL A:220 , GLY A:231 , PHE A:234 , ALA A:261 , HOH A:306 , HOH A:328 , HOH A:331 , HOH A:346 , HOH A:360 , HOH A:390BINDING SITE FOR RESIDUE ATP A 900
2AC2SOFTWARELYS B:39 , ASN B:182 , THR B:200 , GLN B:201 , GLY B:202 , ALA B:203 , GLY B:205 , VAL B:220 , ALA B:230 , GLY B:231 , PHE B:234 , ALA B:261 , HOH B:302 , HOH B:308 , HOH B:311 , HOH B:317 , HOH B:319 , HOH B:324 , HOH B:344 , HOH B:358 , HOH B:370 , HOH B:375 , HOH B:395BINDING SITE FOR RESIDUE ATP B 900
3AC3SOFTWAREASN C:182 , THR C:200 , GLN C:201 , GLY C:202 , ALA C:203 , GLY C:205 , VAL C:220 , GLY C:229 , ALA C:230 , GLY C:231 , PHE C:234 , ALA C:261 , HOH C:300 , HOH C:303 , HOH C:304 , HOH C:330 , HOH C:336 , HOH C:360 , HOH C:377 , HOH C:387 , HOH C:388 , HOH C:391 , HOH C:393BINDING SITE FOR RESIDUE ATP C 900
4AC4SOFTWARETHR C:10 , ASP C:12 , GLY C:38 , ASN C:42 , SER C:93 , ASP C:232 , HOH C:330 , HOH C:367BINDING SITE FOR RESIDUE GOL C 501
5AC5SOFTWARELYS D:39 , ASN D:182 , THR D:200 , GLN D:201 , GLY D:202 , ALA D:203 , GLY D:205 , VAL D:220 , ALA D:230 , GLY D:231 , PHE D:234 , ALA D:261 , HOH D:300 , HOH D:316 , HOH D:328 , HOH D:334 , HOH D:353 , HOH D:356 , HOH D:358 , HOH D:361BINDING SITE FOR RESIDUE ATP D 900
6AC6SOFTWARETHR D:10 , ASP D:12 , GLY D:38 , ASN D:42 , SER D:93 , ASP D:232 , HOH D:356BINDING SITE FOR RESIDUE GOL D 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Leu A:81 -Pro A:82
2Ser A:163 -Pro A:164
3Leu B:81 -Pro B:82
4Ser B:163 -Pro B:164
5Leu C:81 -Pro C:82
6Ser C:163 -Pro C:164
7Glu D:76 -Pro D:77
8Leu D:81 -Pro D:82
9Ser D:163 -Pro D:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IKH)

(-) 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:286
 aligned with A6T989_KLEP7 | A6T989 from UniProtKB/TrEMBL  Length:290

    Alignment length:286
                             1                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279      
         A6T989_KLEP7     - -MRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLMLLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFSLDEMIPHMADAVAGDILLQQGNFSLDKTRALFQYARSRGMTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVMLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLT 285
               SCOP domains d3ikha_ A: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeeee.........eee.eeeeeeeehhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh..eee.........eeeeee.......eeeeehhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeeeehhhhhhhh.....eeeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ikh A  -2 SLRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLmLLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFSLDEmIPHmADAVAGDILLQQGNFSLDKTRALFQYARSRGmTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVmLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLT 285
                             ||      9        19        29        39        49        59        69        79        89        99       109       119|   |  129       139       149      |159       169       179       189       199       209       219       229       239       249       259       269       279      
                             ||                                                                           79-MSE                                  120-MSE                             156-MSE                                                                           238-MSE                                           
                            -1|                                                                                                                       124-MSE                                                                                                                                                             
                              2                                                                                                                                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with A6T989_KLEP7 | A6T989 from UniProtKB/TrEMBL  Length:290

    Alignment length:285
                                    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     
         A6T989_KLEP7     1 MRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLMLLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFSLDEMIPHMADAVAGDILLQQGNFSLDKTRALFQYARSRGMTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVMLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLT 285
               SCOP domains d3ikhb_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeee.........eeeeeeeeeeeehhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh..eee.........eeeeee...--..eeee.hhhhhh.hhhhhhhhhh......eeee....hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeeeehhhhhhhh.....eeeee....eeeeee..eeeeee..........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ikh B  -1 LRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLmLLPDGHFNQHSDTSIILNSA--DNAIITTTAAADTFSLDEmIPHmADAVAGDILLQQGNFSLDKTRALFQYARSRGmTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVmLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLT 285
                            ||      10        20        30        40        50        60        70        80        90        |- |     110       120   |   130       140       150     | 160       170       180       190       200       210       220       230       240       250       260       270       280     
                           -1|                                                                           79-MSE              99  |               120-MSE                             156-MSE                                                                           238-MSE                                           
                             2                                                                                                 102                   124-MSE                                                                                                                                                             

Chain C from PDB  Type:PROTEIN  Length:285
 aligned with A6T989_KLEP7 | A6T989 from UniProtKB/TrEMBL  Length:290

    Alignment length:285
                                    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     
         A6T989_KLEP7     1 MRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLMLLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFSLDEMIPHMADAVAGDILLQQGNFSLDKTRALFQYARSRGMTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVMLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLT 285
               SCOP domains d3ikhc_ C: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeeee........eee.eeeeeeeehhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh...eee..........eeeeeee.....eeee.hhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeeeehhhhhhhh.....eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ikh C  -1 LRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLmLLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFSLDEmIPHmADAVAGDILLQQGNFSLDKTRALFQYARSRGmTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVmLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLT 285
                            ||      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     
                           -1|                                                                           79-MSE                                  120-MSE                             156-MSE                                                                           238-MSE                                           
                             2                                                                                                                       124-MSE                                                                                                                                                             

Chain D from PDB  Type:PROTEIN  Length:286
 aligned with A6T989_KLEP7 | A6T989 from UniProtKB/TrEMBL  Length:290

    Alignment length:286
                             1                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279      
         A6T989_KLEP7     - -MRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLMLLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFSLDEMIPHMADAVAGDILLQQGNFSLDKTRALFQYARSRGMTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVMLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLT 285
               SCOP domains d3ikhd_ D: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeeee.........eee.eeeeeeeehhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh...eee..........eeeeee......eeeeehhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.eeeeehhhhhhhh.....eeeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ikh D  -2 SLRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLmLLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFSLDEmIPHmADAVAGDILLQQGNFSLDKTRALFQYARSRGmTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVmLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLT 285
                             ||      9        19        29        39        49        59        69        79        89        99       109       119|   |  129       139       149      |159       169       179       189       199       209       219       229       239       249       259       269       279      
                            -1|                                                                           79-MSE                                  120-MSE                             156-MSE                                                                           238-MSE                                           
                              2                                                                                                                       124-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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A6T989_KLEP7 | A6T989)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A6T989_KLEP7 | A6T9893i3y

(-) 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-11206L RELATED DB: TARGETDB