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(-) Description

Title :  CRYSTAL STRUCTURE OF INORGANIC POLYPHOSPHATE/ATP-GLUCOMANNOKINASE FROM ARTHROBACTER SP. STRAIN KM AT 1.8 A RESOLUTION
 
Authors :  T. Mukai, S. Kawai, S. Mori, B. Mikami, K. Murata
Date :  24 Aug 04  (Deposition) - 28 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Polyphosphate, Glucomannokinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Mukai, S. Kawai, S. Mori, B. Mikami, K. Murata
Crystal Structure Of Bacterial Inorganic Polyphosphate/Atp-Glucomannokinase: Insights Into Kinase Evolution
J. Biol. Chem. V. 279 50591 2004
PubMed-ID: 15377666  |  Reference-DOI: 10.1074/JBC.M408126200

(-) Compounds

Molecule 1 - INORGANIC POLYPHOSPHATE/ATP-GLUCOMANNOKINASE
    Chains: A, B
    EC Number: 2.7.1.63
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B-GMK
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTHROBACTER SP.
    Organism Taxid: 184230
    Strain: KM

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:83 , GLY A:84 , ALA A:95 , ASN A:96 , ASN A:122 , ASP A:123 , ILE A:153 , GLY A:154 , GLU A:168 , HIS A:171 , GLU A:180 , HOH A:306 , HOH A:309 , HOH A:314 , HOH A:358BINDING SITE FOR RESIDUE BGC A 290
2AC2SOFTWAREGLY A:21 , GLY A:150 , THR A:151 , HOH A:358 , HOH A:384 , HOH A:471BINDING SITE FOR RESIDUE PO4 A 280
3AC3SOFTWARETHR A:22 , LYS A:25 , ARG A:42 , HIS B:177BINDING SITE FOR RESIDUE PO4 A 281
4AC4SOFTWAREPRO B:83 , GLY B:84 , ALA B:95 , ASN B:96 , ASN B:122 , ASP B:123 , ILE B:153 , GLY B:154 , GLU B:168 , HIS B:171 , GLU B:180 , HOH B:318 , HOH B:319 , HOH B:323 , HOH B:354BINDING SITE FOR RESIDUE BGC B 291
5AC5SOFTWAREGLY B:20 , GLY B:21 , GLY B:150 , THR B:151 , HOH B:354 , HOH B:442 , HOH B:466 , HOH B:511BINDING SITE FOR RESIDUE PO4 B 282
6AC6SOFTWARETHR B:22 , LYS B:25 , ARG B:42 , HOH B:466BINDING SITE FOR RESIDUE PO4 B 283

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:47 -Pro A:48
2Gln B:47 -Pro B:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WOQ)

(-) 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:253
 aligned with Q7WT42_ARTSK | Q7WT42 from UniProtKB/TrEMBL  Length:267

    Alignment length:253
                                    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   
         Q7WT42_ARTSK    11 NAPLIGIDIGGTGIKGGIVDLKKGKLLGERFRVPTPQPATPESVAEAVALVVAELSARPEAPAAGSPVGVTFPGIIQHGVVHSAANVDKSWLNTDIDALLTARLGRPVEVINDADAAGLAEARYGAGAGVKGTVLVITLGTGIGSAFIFDGKLVPNAELGHLEIDGHDAETKASAVARERDGLSWDEYSVLLQRYFSHVEFLFSPELFIVGGGISKRADEYLPNLRLRTPIVPAVLRNEAGIVGAAIEIALQH 263
               SCOP domains d1woqa1 A:11-139 Inorganic polyphosphate/ATP-glucomannokinase PPGMK                                                              d1woqa2 A:140-263 Inorganic polyphosphate/ATP-glucomannokinase PPGMK                                                         SCOP domains
               CATH domains 1woqA01 A:11-122  [code=3.30.420.40, no name defined]                                                           1woqA02 A:123-263  [code=3.30.420.40, no name defined]                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...eeeeeeee....eeeeeeeeee.....hhhhhhhhhhhhhhhhhh..........eeeee...ee..ee......hhhhh..hhhhhhhhhhh..eeeeehhhhhhhhhhhh........eeeeeee...eeeeeee..eee...hhhh.ee..eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1woq A  11 NAPLIGIDIGGTGIKGGIVDLKKGKLLGERFRVPTPQPATPESVAEAVALVVAELSARPEAPAAGSPVGVTFPGIIQHGVVHSAANVDKSWLNTDIDALLTARLGRPVEVINDADAAGLAEARYGAGAGVKGTVLVITLGTGIGSAFIFDGKLVPNAELGHLEIDGHDAETKASAVARERDGLSWDEYSVLLQRYFSHVEFLFSPELFIVGGGISKRADEYLPNLRLRTPIVPAVLRNEAGIVGAAIEIALQH 263
                                    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   


Chain B from PDB  Type:PROTEIN  Length:253
 aligned with Q7WT42_ARTSK | Q7WT42 from UniProtKB/TrEMBL  Length:267

    Alignment length:253
                                    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   
         Q7WT42_ARTSK    11 NAPLIGIDIGGTGIKGGIVDLKKGKLLGERFRVPTPQPATPESVAEAVALVVAELSARPEAPAAGSPVGVTFPGIIQHGVVHSAANVDKSWLNTDIDALLTARLGRPVEVINDADAAGLAEARYGAGAGVKGTVLVITLGTGIGSAFIFDGKLVPNAELGHLEIDGHDAETKASAVARERDGLSWDEYSVLLQRYFSHVEFLFSPELFIVGGGISKRADEYLPNLRLRTPIVPAVLRNEAGIVGAAIEIALQH 263
               SCOP domains d1woqb1 B:11-139 Inorganic polyphosphate/ATP-glucomannokinase PPGMK                                                              d1woqb2 B:140-263 Inorganic polyphosphate/ATP-glucomannokinase PPGMK                                                         SCOP domains
               CATH domains 1woqB01 B:11-122  [code=3.30.420.40, no name defined]                                                           1woqB02 B:123-263  [code=3.30.420.40, no name defined]                                                                                        CATH domains
           Pfam domains (1) -----ROK-1woqB01 B:16-187                                                                                                                                                        ---------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----ROK-1woqB02 B:16-187                                                                                                                                                        ---------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee...eeeeeeee....ee....eeee.....hhhhhhhhhhhhhhhhhh..........eeeee...ee..ee......hhhhh..hhhhhhhhhhh..eeeeehhhhhhhhhhhh........eeeeeee...eeeeeee..eee...hhhh.ee..eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.....eee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1woq B  11 NAPLIGIDIGGTGIKGGIVDLKKGKLLGERFRVPTPQPATPESVAEAVALVVAELSARPEAPAAGSPVGVTFPGIIQHGVVHSAANVDKSWLNTDIDALLTARLGRPVEVINDADAAGLAEARYGAGAGVKGTVLVITLGTGIGSAFIFDGKLVPNAELGHLEIDGHDAETKASAVARERDGLSWDEYSVLLQRYFSHVEFLFSPELFIVGGGISKRADEYLPNLRLRTPIVPAVLRNEAGIVGAAIEIALQH 263
                                    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
   Legend:   → Mismatch (orange background)
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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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7WT42_ARTSK | Q7WT42)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
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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