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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRIDOXAMINE KINASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - PYRIDOXAMINE KINASE
    Chains: A, B, C, D
    EC Number: 2.7.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PDXY, B1636
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PM KINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 42)

Asymmetric Unit (4, 42)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2CSD4Mod. Amino Acid3-SULFINOALANINE
3MSE32Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 21)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CSD2Mod. Amino Acid3-SULFINOALANINE
3MSE16Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (4, 21)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CSD2Mod. Amino Acid3-SULFINOALANINE
3MSE16Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:220 , GLY A:221 , VAL A:222 , GLY A:223 , ASP A:224 , HOH A:530BINDING SITE FOR RESIDUE SO4 A 298
2AC2SOFTWAREGLY B:221 , VAL B:222 , GLY B:223 , ASP B:224 , BME B:300 , HOH B:343 , HOH B:367 , HOH B:450 , HOH B:512 , HOH B:536BINDING SITE FOR RESIDUE SO4 B 298
3AC3SOFTWAREGLY C:221 , VAL C:222 , GLY C:223 , ASP C:224BINDING SITE FOR RESIDUE SO4 C 298
4AC4SOFTWAREGLY D:221 , VAL D:222 , GLY D:223 , ASP D:224 , BME D:300 , HOH D:337 , HOH D:520 , HOH D:523BINDING SITE FOR RESIDUE SO4 D 298
5AC5SOFTWARECYS B:122 , ASP B:224 , SO4 B:298BINDING SITE FOR RESIDUE BME B 300
6AC6SOFTWARETYR D:83 , CYS D:122 , VAL D:220 , ASP D:224 , SO4 D:298 , HOH D:357 , HOH D:523BINDING SITE FOR RESIDUE BME D 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VI9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VI9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VI9)

(-) Exons   (0, 0)

(no "Exon" information available for 1VI9)

(-) 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:288
 aligned with PDXY_ECOLI | P77150 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:288
                                                                                                                                                                                                                                                                                                                        287 
                                    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      | 
           PDXY_ECOLI     1 MMKNILAIQSHVVYGHAGNSAAEFPMRRLGANVWPLNTVQFSNHTQYGKWTGCVMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVMGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMVTTKAMQEYELQVVAAQDRIAKPEHYFSATKL-   -
               SCOP domains d1vi9a_ A: Pyridoxamine kinase                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1vi9A00 A:1-288  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee........hhhhhhhhhhhh..eeeeee.eee..hhhhh...eee.hhhhhhhhhhhhhhh.hhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeee....ee...ee....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeee..hhhhh....eeeeeee....eeeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh.......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi9 A   1 LmKNILAIQSHVVYGHAGNSAAEFPmRRLGANVWPLNTVQFSNHTQYGKWTGcVmPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVmGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEmLLVTADEAWHISRPLVDFGmRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEImVTTKAmQEYELQVVAAQDRIAKPEHYFSATKLE 288
                             |      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        
                             |                      26-MSE                     53-CSD                                                       115-MSE                                                                          196-MSE             216-MSE                                255-MSE |                           
                             2-MSE                                               55-MSE                                                                                                                                                                                                       261-MSE                       


Chain B from PDB  Type:PROTEIN  Length:288
 aligned with PDXY_ECOLI | P77150 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:288
                                                                                                                                                                                                                                                                                                                        287 
                                    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      | 
           PDXY_ECOLI     1 MMKNILAIQSHVVYGHAGNSAAEFPMRRLGANVWPLNTVQFSNHTQYGKWTGCVMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVMGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMVTTKAMQEYELQVVAAQDRIAKPEHYFSATKL-   -
               SCOP domains d1vi9b_ B: Pyridoxamine kinase                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1vi9B00 B:1-288  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..hhhhh...eee.hhhhhhhhhhhhhhh.hhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeee.....hhhhh.....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhh....eeee..hhhhh....eeeeeee....eeeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi9 B   1 LmKNILAIQSHVVYGHAGNSAAEFPmRRLGANVWPLNTVQFSNHTQYGKWTGcVmPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVmGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEmLLVTADEAWHISRPLVDFGmRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEImVTTKAmQEYELQVVAAQDRIAKPEHYFSATKLE 288
                             |      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        
                             2-MSE                  26-MSE                     53-CSD                                                       115-MSE                                                                          196-MSE             216-MSE                                255-MSE |                           
                                                                                 55-MSE                                                                                                                                                                                                       261-MSE                       


Chain C from PDB  Type:PROTEIN  Length:288
 aligned with PDXY_ECOLI | P77150 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:288
                                                                                                                                                                                                                                                                                                                        287 
                                    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      | 
           PDXY_ECOLI     1 MMKNILAIQSHVVYGHAGNSAAEFPMRRLGANVWPLNTVQFSNHTQYGKWTGCVMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVMGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMVTTKAMQEYELQVVAAQDRIAKPEHYFSATKL-   -
               SCOP domains d1vi9c_ C: Pyridoxamine kinase                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1vi9C00 C:1-288  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee........hhhhhhhhhhhh..eeeeee.eee..hhhhh...eee.hhhhhhhhhhhhhhh.hhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeee....ee...ee..hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee..hhhhh....eeeeeee....eeeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi9 C   1 LmKNILAIQSHVVYGHAGNSAAEFPmRRLGANVWPLNTVQFSNHTQYGKWTGcVmPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVmGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEmLLVTADEAWHISRPLVDFGmRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEImVTTKAmQEYELQVVAAQDRIAKPEHYFSATKLE 288
                             |      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        
                             2-MSE                  26-MSE                     53-CSD                                                       115-MSE                                                                          196-MSE             216-MSE                                255-MSE |                           
                                                                                 55-MSE                                                                                                                                                                                                       261-MSE                       


Chain D from PDB  Type:PROTEIN  Length:288
 aligned with PDXY_ECOLI | P77150 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:288
                                                                                                                                                                                                                                                                                                                        287 
                                    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      | 
           PDXY_ECOLI     1 MMKNILAIQSHVVYGHAGNSAAEFPMRRLGANVWPLNTVQFSNHTQYGKWTGCVMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVMGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMVTTKAMQEYELQVVAAQDRIAKPEHYFSATKL-   -
               SCOP domains d1vi9d_ D: Pyridoxamine kinase                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1vi9D00 D:1-288  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee........hhhhhhhhhhhh..eeeeee.eee..hhhhh...eee.hhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeee.....hhhhh.....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeee..hhhhh....eeeeeee....eeeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi9 D   1 LmKNILAIQSHVVYGHAGNSAAEFPmRRLGANVWPLNTVQFSNHTQYGKWTGcVmPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVmGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEmLLVTADEAWHISRPLVDFGmRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEImVTTKAmQEYELQVVAAQDRIAKPEHYFSATKLE 288
                             |      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        
                             2-MSE                  26-MSE                     53-CSD                                                       115-MSE                                                                          196-MSE             216-MSE                                255-MSE |                           
                                                                                 55-MSE                                                                                                                                                                                                       261-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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VI9)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PDXY_ECOLI | P77150)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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: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:0009443    pyridoxal 5'-phosphate salvage    Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
    GO:0042817    pyridoxal metabolic process    The chemical reactions and pathways involving 3-hydroxy-5-(hydroxymethyl)-2-methyl-4-pyridinecarboxaldehyde, one of the vitamin B6 compounds. Pyridoxal, pyridoxamine and pyridoxine are collectively known as vitamin B6, and are efficiently converted to the biologically active form of vitamin B6, pyridoxal phosphate.
    GO:0042819    vitamin B6 biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1vi9
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  PDXY_ECOLI | P77150
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  2.7.1.35
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PDXY_ECOLI | P77150: 1td2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VI9)