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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCERATE KINASE (EC 2.7.1.31) (TM1585) FROM THERMOTOGA MARITIMA AT 2.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  07 Oct 05  (Deposition) - 08 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.53
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tm1585, Glycerate Kinase (Ec 2. 7. 1. 31), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Schwarzenbacher, D. Mcmullan, S. S. Krishna, Q. Xu, M. D. Miller, J. M. Canaves, M. A. Elsliger, R. Floyd, S. K. Grzechnik, L. Jaroszewski, H. E. Klock, E. Koesema, J. S. Kovarik, A. Kreusch, P. Kuhn, T. M. Mcphillips, A. T. Morse, K. Quijano, G. Spraggon, R. C. Stevens, H. Van Den Bedem, G. Wolf, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Crystal Structure Of A Glycerate Kinase (Tm1585) From Thermotoga Maritima At 2. 70 A Resolution Reveals A New Fold
Proteins V. 65 243 2006
PubMed-ID: 16865707  |  Reference-DOI: 10.1002/PROT.21058

(-) Compounds

Molecule 1 - GLYCERATE KINASE, PUTATIVE
    Chains: A, B
    EC Number: 2.7.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1585
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2B8N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B8N)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1His A:90 -Pro A:91
2Phe A:178 -Pro A:179
3Arg A:299 -Pro A:300
4Lys A:303 -Pro A:304
5His B:90 -Pro B:91
6Phe B:178 -Pro B:179
7Arg B:299 -Pro B:300
8Lys B:303 -Pro B:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B8N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B8N)

(-) Exons   (0, 0)

(no "Exon" information available for 2B8N)

(-) 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:414
 aligned with GCK_THEMA | Q9X1S1 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:414
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413    
            GCK_THEMA     4 PESLKKLAIEIVKKSIEAVFPDRAVKETLPKLNLDRVILVAVGKAAWRMAKAAYEVLGKKIRKGVVVTKYGHSEGPIDDFEIYEAGHPVPDENTIKTTRRVLELVDQLNENDTVLFLLSGGGSSLFELPLEGVSLEEIQKLTSALLKSGASIEEINTVRKHLSQVKGGRFAERVFPAKVVALVLSDVLGDRLDVIASGPAWPDSSTSEDALKVLEKYGIETSESVKRAILQETPKHLSNVEIHLIGNVQKVCDEAKSLAKEKGFNAEIITTSLDCEAREAGRFIASIMKEVKFKDRPLKKPAALIFGGETVVHVKGNGIGGRNQELALSAAIALEGIEGVILCSAGTDGTDGPTDAAGGIVDGSTAKTLKAMGEDPYQYLKNNDSYNALKKSGALLITGPTGTNVNDLIIGLIV 417
               SCOP domains d2b8na_ A: Putative glycerate kinase (hypothetical protein TM1585)                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2b8nA01            2b8nA02 A:23-249  [code=3.40.50.10180, no name defined]                                                                                                                                                                            2b8nA01 A:4-22,A:250-417 Glycerate kinase like, domain 1                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh..eeeeeeeee...........eeeee.....hhhhhhhhhhhhhhhh......eeeeee..hhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhh......hhhhhhhh..eeeeeee.........hhhhh.......hhhhhhhhhhhh....hhhhhhhhh.........eeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhh......eeeeeee............hhhhhhhhhhhhhh.....eeeeeee...........eeeee.hhhhhhhhh..hhhhhhhh.hhhhhhhhh..ee..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b8n A   4 PESLKKLAIEIVKKSIEAVFPDRAVKETLPKLNLDRVILVAVGKAAWRmAKAAYEVLGKKIRKGVVVTKYGHSEGPIDDFEIYEAGHPVPDENTIKTTRRVLELVDQLNENDTVLFLLSGGGSSLFELPLEGVSLEEIQKLTSALLKSGASIEEINTVRKHLSQVKGGRFAERVFPAKVVALVLSDVLGDRLDVIASGPAWPDSSTSEDALKVLEKYGIETSESVKRAILQETPKHLSNVEIHLIGNVQKVCDEAKSLAKEKGFNAEIITTSLDCEAREAGRFIASImKEVKFKDRPLKKPAALIFGGETVVHVKGNGIGGRNQELALSAAIALEGIEGVILCSAGTDGTDGPTDAAGGIVDGSTAKTLKAmGEDPYQYLKNNDSYNALKKSGALLITGPTGTNVNDLIIGLIV 417
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373 |     383       393       403       413    
                                                                           52-MSE                                                                                                                                                                                                                                        291-MSE                                                                             375-MSE                                      


Chain B from PDB  Type:PROTEIN  Length:414
 aligned with GCK_THEMA | Q9X1S1 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:414
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413    
            GCK_THEMA     4 PESLKKLAIEIVKKSIEAVFPDRAVKETLPKLNLDRVILVAVGKAAWRMAKAAYEVLGKKIRKGVVVTKYGHSEGPIDDFEIYEAGHPVPDENTIKTTRRVLELVDQLNENDTVLFLLSGGGSSLFELPLEGVSLEEIQKLTSALLKSGASIEEINTVRKHLSQVKGGRFAERVFPAKVVALVLSDVLGDRLDVIASGPAWPDSSTSEDALKVLEKYGIETSESVKRAILQETPKHLSNVEIHLIGNVQKVCDEAKSLAKEKGFNAEIITTSLDCEAREAGRFIASIMKEVKFKDRPLKKPAALIFGGETVVHVKGNGIGGRNQELALSAAIALEGIEGVILCSAGTDGTDGPTDAAGGIVDGSTAKTLKAMGEDPYQYLKNNDSYNALKKSGALLITGPTGTNVNDLIIGLIV 417
               SCOP domains d2b8nb_ B: Putative glycerate kinase (hypothetical protein TM1585)                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2b8nB01            2b8nB02 B:23-249  [code=3.40.50.10180, no name defined]                                                                                                                                                                            2b8nB01 B:4-22,B:250-417 Glycerate kinase like, domain 1                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh..eeeeeeeee...........eeeee.....hhhhhhhhhhhhhhhh......eeeeee..hhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhh..eeeeeee.........hhhhh.......hhhhhhhhhhhh....hhhhhhhhh.........eeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhh......eeeeeee............hhhhhhhhhhhhhh.....eeeeeee...........eeeee.hhhhhhhhh..hhhhhhhh.hhhhhhhhh..ee..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b8n B   4 PESLKKLAIEIVKKSIEAVFPDRAVKETLPKLNLDRVILVAVGKAAWRmAKAAYEVLGKKIRKGVVVTKYGHSEGPIDDFEIYEAGHPVPDENTIKTTRRVLELVDQLNENDTVLFLLSGGGSSLFELPLEGVSLEEIQKLTSALLKSGASIEEINTVRKHLSQVKGGRFAERVFPAKVVALVLSDVLGDRLDVIASGPAWPDSSTSEDALKVLEKYGIETSESVKRAILQETPKHLSNVEIHLIGNVQKVCDEAKSLAKEKGFNAEIITTSLDCEAREAGRFIASImKEVKFKDRPLKKPAALIFGGETVVHVKGNGIGGRNQELALSAAIALEGIEGVILCSAGTDGTDGPTDAAGGIVDGSTAKTLKAmGEDPYQYLKNNDSYNALKKSGALLITGPTGTNVNDLIIGLIV 417
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373 |     383       393       403       413    
                                                                           52-MSE                                                                                                                                                                                                                                        291-MSE                                                                             375-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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B8N)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GCK_THEMA | Q9X1S1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008887    glycerate kinase activity    Catalysis of the reaction: D-glycerate + ATP = 3-phospho-D-glycerate + ADP + 2 H(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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