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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOKINASE IN COMPLEX WITH D-RIBOSE FROM KLEBSIELLA PNEUMONIAE
 
Authors :  L. Satyanarayana, S. K. Burley, S. Swaminathan, New York Sgx Resear For Structural Genomics (Nysgxrc)
Date :  01 Jul 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
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, 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 D-Ribose From Klebsiella Pneumoniae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CARBOHYDRATE KINASE
    Atcc: 700721
    Chains: A, B, C, D
    EC Number: 2.7.1.15
    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: 5340552, KPN78578_16990, KPN_01729
    Organism Scientific: KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE MGH 78578
    Organism Taxid: 272620
    Strain: 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  (4, 28)

Asymmetric Unit (4, 28)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE20Mod. Amino AcidSELENOMETHIONINE
3RIB1Ligand/IonRIBOSE
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3RIB-1Ligand/IonRIBOSE
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 15)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3RIB1Ligand/IonRIBOSE
4SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:39 , GLY B:229 , ALA B:230 , GLY B:231 , ASP B:232BINDING SITE FOR RESIDUE SO4 B 298
2AC2SOFTWAREPHE B:86 , ASN B:87BINDING SITE FOR RESIDUE SO4 B 299
3AC3SOFTWARESER B:26 , SER D:163 , VAL D:165 , GLU D:185BINDING SITE FOR RESIDUE SO4 B 300
4AC4SOFTWAREILE C:199 , TRP C:207 , VAL C:209 , ARG C:214 , HOH C:354BINDING SITE FOR RESIDUE SO4 C 1
5AC5SOFTWARELYS C:39 , THR C:228 , GLY C:229 , ALA C:230 , GLY C:231 , ASP C:232 , GOL C:501BINDING SITE FOR RESIDUE SO4 C 298
6AC6SOFTWARETHR C:10 , ASP C:12 , GLY C:38 , ASN C:42 , SER C:93 , ASP C:232 , SO4 C:298BINDING SITE FOR RESIDUE GOL C 501
7AC7SOFTWARELYS D:39 , GLY D:229 , ALA D:230 , GLY D:231 , ASP D:232 , RIB D:311BINDING SITE FOR RESIDUE SO4 D 298
8AC8SOFTWARETHR D:10 , ASP D:12 , GLY D:37 , GLY D:38 , LYS D:39 , ASN D:42 , SER D:93 , THR D:107 , ASP D:232 , SO4 D:298BINDING SITE FOR RESIDUE RIB D 311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I3Y)

(-) Cis Peptide Bonds  (8, 8)

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
7Leu D:81 -Pro D:82
8Ser D:163 -Pro D:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3I3Y)

(-) 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: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 d3i3ya_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeee.........eee.eeeeeeeehhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eee.........eeeeee.......eeeee.hhhhhh....hhhhhh......eeee....hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhh.eeeeehhhhh........eeeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3y A  -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     
                            ||                                                                           79-MSE                                  120-MSE                             156-MSE                                                                           238-MSE                                           
                           -1|                                                                                                                       124-MSE                                                                                                                                                             
                             2                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:282
 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 d3i3yb_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeeee.........eee.eeeeeeeehhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhh....eee.........eeeee.--...-..eeee.......hhhhhhhhhh......eeee....hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeeeehhhhhhhh.....eeeee....eeeee....eeeee..........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3y B  -1 LRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLmLLPDGHFNQHSDTSIIL--ADG-NAIITTTAAADTFSLDEmIPHmADAVAGDILLQQGNFSLDKTRALFQYARSRGmTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVmLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLT 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           96 99 | |              120-MSE                             156-MSE                                                                           238-MSE                                           
                             2                                                                                                101 |                  124-MSE                                                                                                                                                             
                                                                                                                                103                                                                                                                                                                                      


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 d3i3yc_ C: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeeeee........eee.eeeeeeeehhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhh....eee..........eeeeeee.....eeee.hhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeeehhhhhhhhh.....eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3y 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: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 d3i3yd_ D: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeee.........eee.eeeeeeee..hhhhhhhhhhh...eeee.....hhhhhhhhhhhhh...eee..........eeeeee......eeee.hhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.eeeeehhhhhhhh.....eeeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3y D  -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
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I3Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I3Y)

(-) 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 | A6T989: 3ikh

(-) Related Entries Specified in the PDB File

3h49 CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE (APO FORM) FROM E.COLI AT 1.8A RESOLUTION RELATED ID: NYSGXRC-11206L RELATED DB: TARGETDB