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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AN ADP COMPLEX OF BACILLUS SUBTILIS PYRIDOXAL KINASE PROVIDES EVIDENCE FOR THE PARRALEL EMERGENCE OF ENZYME ACTIVITY DURING EVOLUTION
 
Authors :  J. A. Newman, S. K. Das, S. E. Sedelnikova, D. W. Rice
Date :  24 Aug 06  (Deposition) - 19 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E  (2x)
Keywords :  Adp Complex, Pdxk, Thid, Ribokinase Superfamily, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Newman, S. K. Das, S. E. Sedelnikova, D. W. Rice
The Crystal Structure Of An Adp Complex Of Bacillus Subtilis Pyridoxal Kinase Provides Evidence For The Parallel Emergence Of Enzyme Activity During Evolution.
J. Mol. Biol. V. 363 520 2006
PubMed-ID: 16978644  |  Reference-DOI: 10.1016/J.JMB.2006.08.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOMETHYLPYRIMIDINE KINASE
    Chains: A, C, D, B, E
    EC Number: 2.7.4.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PTB361
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: THID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168
    Synonym: HMP-PHOSPHATE KINASE, HMP-P KINASE

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): AB   
Biological Unit 2 (1x):   CD 
Biological Unit 3 (2x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1ADP5Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:141 , THR A:178 , GLY A:180 , GLY A:181 , LYS A:182 , ALA A:188 , ASP A:190 , GLU A:204 , ILE A:206 , ALA A:214 , GLY A:215 , LYS A:240 , ILE A:243 , ILE A:247BINDING SITE FOR RESIDUE ADP A 301
2AC2SOFTWAREASN C:141 , THR C:178 , GLY C:180 , GLY C:181 , LYS C:182 , ALA C:188 , ASP C:190 , GLU C:204 , ILE C:206 , ALA C:214 , GLY C:215 , LYS C:240 , ILE C:243 , ILE C:247BINDING SITE FOR RESIDUE ADP C 401
3AC3SOFTWAREASN D:141 , THR D:178 , GLY D:180 , GLY D:181 , LYS D:182 , ALA D:188 , ASP D:190 , GLU D:204 , ILE D:206 , ALA D:214 , GLY D:215 , LYS D:240 , ILE D:243 , ILE D:247BINDING SITE FOR RESIDUE ADP D 501
4AC4SOFTWAREASN B:141 , THR B:178 , GLY B:180 , GLY B:181 , LYS B:182 , ALA B:188 , ASP B:190 , GLU B:204 , ILE B:206 , ALA B:214 , GLY B:215 , LYS B:240 , ILE B:243 , ILE B:247BINDING SITE FOR RESIDUE ADP B 601
5AC5SOFTWAREASN E:141 , THR E:178 , GLY E:180 , GLY E:181 , LYS E:182 , ALA E:188 , ASP E:190 , GLU E:204 , ILE E:206 , ALA E:214 , GLY E:215 , LYS E:240 , ILE E:243 , ILE E:247BINDING SITE FOR RESIDUE ADP E 701

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:112 -C:112

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I5B)

(-) Exons   (0, 0)

(no "Exon" information available for 2I5B)

(-) 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:269
 aligned with PDXK_BACSU | P39610 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:269
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262         
           PDXK_BACSU     3 MHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRLNQQS 271
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i5bA00 A:3-271  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeeeee.......eeeee.hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh.....hhhhhhhhhhhhhh....eeeee.hhhh....eeeeee....eeeeee.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i5b A   3 MHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRLNQQS 271
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262         


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with PDXK_BACSU | P39610 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:267
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
           PDXK_BACSU     2 SMHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRLN 268
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i5bB00 B:2-268  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....hhhhhhhhhhhhh.eeeeeeeeeeeeee.....eeeeee.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh....eee....---------hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh.....hhhhhhhhhhhhhh....eeeee.hhhh....eeeeee....eeeeee.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i5b B   2 SMHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVM---------YPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRLN 268
                                    11        21        31        41        51        61        71        81        91       101        |-       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
                                                                                                                                      110       120                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:265
 aligned with PDXK_BACSU | P39610 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:265
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262     
           PDXK_BACSU     3 MHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRL 267
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i5bC00 C:3-267  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeeeee.......eeeee.hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh.....hhhhhhhhhhhhhh....eeeee.hhhh....eeeeee....eeeeee.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i5b C   3 MHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRL 267
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262     


Chain D from PDB  Type:PROTEIN  Length:267
 aligned with PDXK_BACSU | P39610 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:267
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
           PDXK_BACSU     2 SMHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRLN 268
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i5bD00 D:2-268  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....hhhhhhhhhhhhh.eeeeeeeeeeeeee.....eeeeee.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh.....hhhhhhhhhhhhhh....eeeee.hhhh....eeeeee....eeeeee.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i5b D   2 SMHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRLN 268
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       


Chain E from PDB  Type:PROTEIN  Length:267
 aligned with PDXK_BACSU | P39610 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:267
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
           PDXK_BACSU     2 SMHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRLN 268
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i5bE00 E:2-268  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....hhhhhhhhhhhhh.eeeeeeeeeeeee.......eeeee.hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh...eee.............hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh.....hhhhhhhhhhhhhh....eeeee.hhhh....eeeeee....eeeeee.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i5b E   2 SMHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESFPLNQYVGPTKHSALRLN 268
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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  (0, 0)

(no "SCOP Domain" information available for 2I5B)

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I5B)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (PDXK_BACSU | P39610)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008972    phosphomethylpyrimidine kinase activity    Catalysis of the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
    GO:0008478    pyridoxal kinase activity    Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
    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:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.

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