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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  M. E. Cuff, X. Xu, H. Zheng, A. M. Edwards, A. Savchenko, A. Joachimiak, M Center For Structural Genomics (Mcsg)
Date :  18 Sep 07  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Sugar Kinase, Ribokinase Family, Atp-Binding Site, Structural Genomics, Agrobacterium Tumefaciens, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, X. Xu, H. Zheng, A. M. Edwards, A. Savchenko, A. Joachimiak
Structure Of A Putative Ribokinase From Agrobacterium Tumefaciens.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR KINASE
    Atcc: 33970
    Chains: A
    EC Number: 2.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED P11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RBSK, AGR_C_4560, ATU2509
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58
    Synonym: AGR_C_4560P

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric Unit (5, 21)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MSE9Mod. Amino AcidSELENOMETHIONINE
5SO45Ligand/IonSULFATE ION
Biological Unit 1 (4, 40)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4MSE18Mod. Amino AcidSELENOMETHIONINE
5SO410Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:239 , THR A:240 , ARG A:275 , TRP A:307 , LEU A:308 , ARG A:310 , HOH A:386 , HOH A:610 , HOH A:631BINDING SITE FOR RESIDUE SO4 A 322
02AC2SOFTWARETRP A:228 , HIS A:237 , ARG A:271 , HOH A:584 , HOH A:595 , HOH A:658BINDING SITE FOR RESIDUE SO4 A 323
03AC3SOFTWAREARG A:56 , HOH A:510 , HOH A:571 , HOH A:661 , HOH A:668BINDING SITE FOR RESIDUE SO4 A 324
04AC4SOFTWAREPRO A:171 , VAL A:172 , GLU A:173 , ARG A:194BINDING SITE FOR RESIDUE SO4 A 325
05AC5SOFTWAREARG A:97 , ARG A:120BINDING SITE FOR RESIDUE SO4 A 326
06AC6SOFTWAREARG A:75BINDING SITE FOR RESIDUE CL A 327
07AC7SOFTWARETHR A:20 , LEU A:100 , SER A:101 , THR A:102 , HOH A:350BINDING SITE FOR RESIDUE EDO A 328
08AC8SOFTWAREALA A:127 , THR A:129 , ASP A:132 , HOH A:561BINDING SITE FOR RESIDUE EDO A 329
09AC9SOFTWAREGLY A:89 , MSE A:90 , THR A:91 , HOH A:719BINDING SITE FOR RESIDUE EDO A 330
10BC1SOFTWARETHR A:220 , ALA A:221 , GLY A:222 , GLY A:225 , PHE A:256 , SER A:278 , HOH A:374 , HOH A:732BINDING SITE FOR RESIDUE EDO A 331
11BC2SOFTWAREARG A:111 , THR A:249 , HOH A:440BINDING SITE FOR RESIDUE EDO A 332
12BC3SOFTWAREVAL A:17 , ASP A:19 , SER A:101 , ILE A:113 , HOH A:334 , HOH A:457 , HOH A:576 , HOH A:580 , HOH A:723BINDING SITE FOR RESIDUE GOL A 333

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RBC)

(-) 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:306
 aligned with A9CHQ7_AGRFC | A9CHQ7 from UniProtKB/TrEMBL  Length:319

    Alignment length:306
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305      
         A9CHQ7_AGRFC     6 GGKHVLCVGAAVLDTLFRVADMPKGEGKVLPYEVLQIAEGMASSAAYAVHRMGGRASLWGAVGDDETGTRILRDLSESGIDTSGMTVAPGARSALSTIIIDNRGERLIVPFYDHRLHEKKRACTPEDIALFDAVLVDVRWPELALDVLTVARALGKPAILDGDVAPVETLEGLAPAATHIVFSEPAATRLTGLETVKDMLPVLHARYPQTFIAVTAGPAGCWWTEADDPTVHFQTTMQVEAVDTLAAGDIFHGTFALAMAEGMQSRAAVRLSSVAAALKCTVFGGRIGAPTREETEEAMRQWLERE 311
               SCOP domains d2rbca_ A: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2rbcA00 A:6-311  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...eeeeeee..............eeeeeeehhhhhhhhhhhhh..eeeee.eee.hhhhhhhhhhhhhh.ee....eee.....eeeeeee.....eeeeee.hhhhhh.....hhhhhh...eeee...hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh.eeeeehhhhhhhhh..hhhhhhhhhhhhh...eeeee.hhh.eeee......eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rbc A   6 GGKHVLCVGAAVLDTLFRVADmPKGEGKVLPYEVLQIAEGmASSAAYAVHRmGGRASLWGAVGDDETGTRILRDLSESGIDTSGmTVAPGARSALSTIIIDNRGERLIVPFYDHRLHEKKRACTPEDIALFDAVLVDVRWPELALDVLTVARALGKPAILDGDVAPVETLEGLAPAATHIVFSEPAATRLTGLETVKDmLPVLHARYPQTFIAVTAGPAGCWWTEADDPTVHFQTTmQVEAVDTLAAGDIFHGTFALAmAEGmQSRAAVRLSSVAAALKCTVFGGRIGAPTREETEEAmRQWLERE 311
                                    15        25 |      35        45|       55 |      65        75        85    |   95       105       115       125       135       145       155       165       175       185       195       205       215       225       235      |245       255       265  |    275       285       295       305      
                                                27-MSE             46-MSE     57-MSE                           90-MSE                                                                                                           204-MSE                               242-MSE               264-MSE                                 304-MSE   
                                                                                                                                                                                                                                                                                                268-MSE
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  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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (A9CHQ7_AGRFC | A9CHQ7)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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: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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