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(-) Description

Title :  GLYCERATE KINASE FROM NEISSERIA MENINGITIDIS (SEROGROUP A)
 
Authors :  K. R. Rajashankar, R. Kniewel, V. Solorzano, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  13 Jun 04  (Deposition) - 22 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Glycerate Metabolism, Structural Genomics T831, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. R. Rajashankar, R. Kniewel, V. Solorzano, C. D. Lima
Glycerate Kinase From Neisseria Meningitidis (Serogroup A)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCERATE KINASE
    Chains: A, B
    EC Number: 2.7.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET T7
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GLXK, NMA1473
    Organism Scientific: NEISSERIA MENINGITIDIS SEROGROUP A
    Organism Taxid: 65699
    Strain: SEROGROUP A

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:76 , GLY B:67 , SER B:68 , PHE B:69 , GLY B:70 , GLN B:71 , GLU B:73BINDING SITE FOR RESIDUE SO4 A 372
2AC2SOFTWARESER B:9 , PHE B:10 , LYS B:11 , GLU B:286 , GLY B:287 , ARG B:288BINDING SITE FOR RESIDUE SO4 B 372
3AC3SOFTWAREGLY B:132 , GLY B:133 , ASP B:191 , HOH B:423BINDING SITE FOR RESIDUE SO4 B 373
4AC4SOFTWAREGLY A:132 , GLY A:133 , THR A:134 , GLY A:244BINDING SITE FOR RESIDUE SO4 A 373
5AC5SOFTWARESER A:9 , LYS A:11 , GLU A:286 , GLY A:287 , ARG A:288BINDING SITE FOR RESIDUE SO4 A 374
6AC6SOFTWAREGLY A:67 , SER A:68 , PHE A:69 , GLY A:70 , GLN A:71 , GLU A:73 , ARG B:76BINDING SITE FOR RESIDUE SO4 A 375

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TO6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:326 -Pro A:327
2Leu B:326 -Pro B:327

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TO6)

(-) Exons   (0, 0)

(no "Exon" information available for 1TO6)

(-) 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:371
 aligned with GLXK_NEIMA | P57098 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:371
                                    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       290       300       310       320       330       340       350       360       370 
           GLXK_NEIMA     1 MKIVIAPDSFKESLTAQQVAEAIKRGFQQSIADVECLLCPVGDGGEGTVDAIRHSLDLEEKCLQVTGSFGQKEVMRYFQKEQLALFEVADLVGLGKIPLEKRNPLQIQTRGIGELIRHLISQEIKEIYIGVGGTASNDGGIGIAAGLGYQFYDEDGNALPACGQSLLNLASVSTENRYKIPEDVHIRILADVVSPLCGHQGATYTFGKQKGLDSTMFEVVDQAIQDFYEKVSPATLKLKGAGAGGGIAGGLCAFAQASIVSGIDTCLDLIDFDKKVSDVDLVIVGEGRLDRQSLAGKAPIGVAKRTPVGVPVVAICGSLVEDLPSLPFENIQAAFSILEKSEPLEDSLKNASLYLEHTASNIGHLLNMPKI 371
               SCOP domains d1to6a_ A: Glycerate kinase GlxK                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1to6A01 A:1-41,A:271-371                 1to6A02 A:42-270 Glycerate kinase, domain 2                                                                                                                                                                                          1to6A01 A:1-41,A:271-371 Glycerate kinase; domain 1                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........hhhhhhhhhhhhhhhhh...eeee........hhhhhhhh....eeeeeeee.....eeeeeeee...eeeeehhhhhhhhhh...........hhhhhhhhhhhhhh...eeeee.........hhhhhhh...eee.........hhhhhhh..eee...........eeeeee..........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..eeeehhhhhhhhhhhhhhh....eeee...ee.......hhhhhhhh.......eeeee.ee...........eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to6 A   1 MKIVIAPDSFKESLTAQQVAEAIKRGFQQSIADVECLLCPVGDGGEGTVDAIRHSLDLEEKCLQVTGSFGQKEVMRYFQKEQLALFEVADLVGLGKIPLEKRNPLQIQTRGIGELIRHLISQEIKEIYIGVGGTASNDGGIGIAAGLGYQFYDEDGNALPACGQSLLNLASVSTENRYKIPEDVHIRILADVVSPLCGHQGATYTFGKQKGLDSTMFEVVDQAIQDFYEKVSPATLKLKGAGAGGGIAGGLCAFAQASIVSGIDTCLDLIDFDKKVSDVDLVIVGEGRLDRQSLAGKAPIGVAKRTPVGVPVVAICGSLVEDLPSLPFENIQAAFSILEKSEPLEDSLKNASLYLEHTASNIGHLLNMPKI 371
                                    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       290       300       310       320       330       340       350       360       370 


Chain B from PDB  Type:PROTEIN  Length:371
 aligned with GLXK_NEIMA | P57098 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:371
                                    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       290       300       310       320       330       340       350       360       370 
           GLXK_NEIMA     1 MKIVIAPDSFKESLTAQQVAEAIKRGFQQSIADVECLLCPVGDGGEGTVDAIRHSLDLEEKCLQVTGSFGQKEVMRYFQKEQLALFEVADLVGLGKIPLEKRNPLQIQTRGIGELIRHLISQEIKEIYIGVGGTASNDGGIGIAAGLGYQFYDEDGNALPACGQSLLNLASVSTENRYKIPEDVHIRILADVVSPLCGHQGATYTFGKQKGLDSTMFEVVDQAIQDFYEKVSPATLKLKGAGAGGGIAGGLCAFAQASIVSGIDTCLDLIDFDKKVSDVDLVIVGEGRLDRQSLAGKAPIGVAKRTPVGVPVVAICGSLVEDLPSLPFENIQAAFSILEKSEPLEDSLKNASLYLEHTASNIGHLLNMPKI 371
               SCOP domains d1to6b_ B: Glycerate kinase GlxK                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1to6B01 B:1-41,B:271-371                 1to6B02 B:42-270 Glycerate kinase, domain 2                                                                                                                                                                                          1to6B01 B:1-41,B:271-371 Glycerate kinase; domain 1                                                   CATH domains
           Pfam domains (1) Gly_kinase-1to6B01 B:1-370                                                                                                                                                                                                                                                                                                                                                        - Pfam domains (1)
           Pfam domains (2) Gly_kinase-1to6B02 B:1-370                                                                                                                                                                                                                                                                                                                                                        - Pfam domains (2)
         Sec.struct. author .eeee.........hhhhhhhhhhhhhhhhh...eeee........hhhhhhhh....eeeeeeee.....eeeeeeeee..eeeeehhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeeee.........hhhhhhh...eee.........hhhhhhhh.eee...........eeeeee..........hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh....eeee...ee.......hhhhhhhhh......eeeee.ee...........eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to6 B   1 MKIVIAPDSFKESLTAQQVAEAIKRGFQQSIADVECLLCPVGDGGEGTVDAIRHSLDLEEKCLQVTGSFGQKEVMRYFQKEQLALFEVADLVGLGKIPLEKRNPLQIQTRGIGELIRHLISQEIKEIYIGVGGTASNDGGIGIAAGLGYQFYDEDGNALPACGQSLLNLASVSTENRYKIPEDVHIRILADVVSPLCGHQGATYTFGKQKGLDSTMFEVVDQAIQDFYEKVSPATLKLKGAGAGGGIAGGLCAFAQASIVSGIDTCLDLIDFDKKVSDVDLVIVGEGRLDRQSLAGKAPIGVAKRTPVGVPVVAICGSLVEDLPSLPFENIQAAFSILEKSEPLEDSLKNASLYLEHTASNIGHLLNMPKI 371
                                    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       290       300       310       320       330       340       350       360       370
   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  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Gly_kinase] (1)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GLXK_NEIMA | P57098)
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: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: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:0031388    organic acid phosphorylation    The process of introducing one or more phosphate groups into an organic acid.
    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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