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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUCONATE KINASE FROM LACTOBACILLUS ACIDOPHILUS
 
Authors :  Z. Zhang, S. Swaminathan, S. K. Burley, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  20 Feb 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Lba0354, Gluconate Kinase, Lactobacillus Acidophilus, Fggy Kinase Family, Carbohydrate Metabolic Process, Kinase, Transferase, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. Swaminathan, S. K. Burley
The Crystal Structure Of Gluconate Kinase From Lactobacillu Acidophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUCONATE KINASE
    Chains: A
    EC Number: 2.7.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL-STRATAGENE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LBA0354
    Organism Scientific: LACTOBACILLUS ACIDOPHILUS
    Organism Taxid: 272621
    Strain: NCFM

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3GBT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:213 -Pro A:214
2Ala A:343 -Pro A:344

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GBT)

(-) 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:492
 aligned with Q5FM28_LACAC | Q5FM28 from UniProtKB/TrEMBL  Length:494

    Alignment length:492
                             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       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489  
         Q5FM28_LACAC     - -MKYIIGMDVGTTATKGVLYDINGKAVASVSKGYPLIQTKVGQAEEDPKLIFDAVQEIIFDLTQKIDGKIAAISWSSQMHSLIGLGSDDELLTNSITWADNCAKSIVQDAKNRGFAQQIYRKTGMPMHPMAPIYKLLWLKNKKTEVFSQAQKWIGIKEYIIFRLTGKLVTDTTMAAGTGILNLKTLTWDQELLDILKIKKEQLPKIAQPTKVIFPIKTEYVKKLGIDSDTKIILGASDGYLSTIGVNAIDSDHCALNVGTSGAIRTIVDQPKIDPSASYFCYPADKTHYLLGGPVNNGGIVFNWARQTLFDADETPQDFLDVAQTAPAGSRNLIFLPYLGGERAPIWDANARGSFVGLTRMHQKPEMARAVIEGIIFNLYDAASNLIKNTKKPVAINATGGFLKSDFVRQLCANIFNVPIVTMKEQQSGTLAAMFLARQALGLNQDLSEIGQFAQADKVYFPNPKEAATYQKLFPLYCEIRNALAASYGKFS 491
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeee....eeeeeeee...........eehhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhh..eeehhhhh............hhhhhhhhh.hhhhh.eee....ee...hhhhhhhh......eee..eehhhhhhhh.......eeeeee...eeeeeee...........eeeeee..eeeeeeee..hhhhhhhhhhhhh....hhhhhhhhhhh...hhhhheeee...............eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....hhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gbt A   0 SLKYIIGmDVGTTATKGVLYDINGKAVASVSKGYPLIQTKVGQAEEDPKLIFDAVQEIIFDLTQKIDGKIAAISWSSQmHSLIGLGSDDELLTNSITWADNCAKSIVQDAKNRGFAQQIYRKTGmPmHPmAPIYKLLWLKNKKTEVFSQAQKWIGIKEYIIFRLTGKLVTDTTmAAGTGILNLKTLTWDQELLDILKIKKEQLPKIAQPTKVIFPIKTEYVKKLGIDSDTKIILGASDGYLSTIGVNAIDSDHCALNVGTSGAIRTIVDQPKIDPSASYFCYPADKTHYLLGGPVNNGGIVFNWARQTLFDADETPQDFLDVAQTAPAGSRNLIFLPYLGGERAPIWDANARGSFVGLTRmHQKPEmARAVIEGIIFNLYDAASNLIKNTKKPVAINATGGFLKSDFVRQLCANIFNVPIVTmKEQQSGTLAAmFLARQALGLNQDLSEIGQFAQADKVYFPNPKEAATYQKLFPLYCEIRNALAASYGKFS 491
                                   | 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       289       299       309       319       329       339       349       359|     |369       379       389       399       409       419  |    429   |   439       449       459       469       479       489  
                                   7-MSE                                                                 78-MSE                                       124-MSE|                                         173-MSE                                                                                                                                                                                    360-MSE |                                                     422-MSE    433-MSE                                                      
                                                                                                                                                        126-MSE                                                                                                                                                                                                                                         366-MSE                                                                                                                         
                                                                                                                                                           129-MSE
   Legend:   → Mismatch (orange background)
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  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 3GBT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5FM28_LACAC | Q5FM28)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0046316    gluconokinase activity    Catalysis of the reaction: D-gluconate + ATP = 6-phospho-D-gluconate + ADP + 2 H(+).
    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: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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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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