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(-) Description

Title :  STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH AMP-PCP AND PYRIDOXAL
 
Authors :  M. Nodwell, F. Alte, S. A. Sieber, S. Schneider
Date :  12 Sep 13  (Deposition) - 19 Mar 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Transferase, Ribokinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Nodwell, M. F. Koch, F. Alte, S. Schneider, S. A. Sieber
A Subfamily Of Bacterial Ribokinases Utilizes A Hemithioacetal For Pyridoxal Phosphate Salvage.
J. Am. Chem. Soc. V. 136 4992 2014
PubMed-ID: 24601602  |  Reference-DOI: 10.1021/JA411785R

(-) Compounds

Molecule 1 - PHOSPHOMETHYLPYRIMIDINE KINASE
    Atcc: 700699
    Chains: A, B, C, D
    EC Number: 2.7.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: MU50
    Synonym: PYRIDOXAL KINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1ACP4Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2PXL3Ligand/Ion3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE
3SO47Ligand/IonSULFATE ION
4UEG1Ligand/Ion4,5-BIS(HYDROXYMETHYL)-2-METHYL-PYRIDIN-3-OL
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2PXL1Ligand/Ion3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE
3SO43Ligand/IonSULFATE ION
4UEG1Ligand/Ion4,5-BIS(HYDROXYMETHYL)-2-METHYL-PYRIDIN-3-OL
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2PXL2Ligand/Ion3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE
3SO44Ligand/IonSULFATE ION
4UEG-1Ligand/Ion4,5-BIS(HYDROXYMETHYL)-2-METHYL-PYRIDIN-3-OL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:11 , SER A:12 , ASP A:13 , GLY A:19 , CYS A:214 , ACP A:500 , HOH A:2007BINDING SITE FOR RESIDUE PXL A 300
02AC2SOFTWARELYS A:176 , SER A:186 , ASP A:188 , ASP A:202 , MET A:203 , PHE A:204 , GLN A:205 , ASN A:209 , HIS A:210 , GLY A:211 , ALA A:212 , GLY A:213 , CYS A:214 , LYS A:238 , ILE A:245 , PXL A:300 , HOH A:2051 , HOH A:2056BINDING SITE FOR RESIDUE ACP A 500
03AC3SOFTWAREGLY B:11 , SER B:12 , ASP B:13 , GLY B:19 , VAL B:42 , MET B:80 , VAL B:107 , HIS B:210 , CYS B:214 , ACP B:500 , HOH B:2005BINDING SITE FOR RESIDUE PXL B 300
04AC4SOFTWARELYS B:176 , GLY B:178 , SER B:186 , ASP B:188 , ASP B:202 , MET B:203 , PHE B:204 , GLN B:205 , GLN B:206 , ASN B:209 , HIS B:210 , GLY B:211 , ALA B:212 , GLY B:213 , CYS B:214 , LYS B:238 , ILE B:245 , PXL B:300 , HOH B:2053 , HOH B:2054 , HOH B:2062 , HOH B:2085BINDING SITE FOR RESIDUE ACP B 500
05AC5SOFTWAREGLY C:11 , GLY C:19 , CYS C:214 , ACP C:500 , HOH C:2009BINDING SITE FOR RESIDUE PXL C 300
06AC6SOFTWARELYS C:176 , GLY C:178 , LYS C:179 , SER C:186 , ASP C:188 , ASP C:202 , MET C:203 , PHE C:204 , GLN C:205 , ASN C:209 , HIS C:210 , GLY C:211 , ALA C:212 , GLY C:213 , CYS C:214 , LYS C:238 , ILE C:245 , PXL C:300 , HOH C:2047 , HOH C:2048 , HOH C:2058BINDING SITE FOR RESIDUE ACP C 500
07AC7SOFTWAREGLY D:11 , GLY D:19 , VAL D:42 , VAL D:109 , CYS D:110 , HIS D:210 , CYS D:214 , HOH D:2003 , HOH D:2016BINDING SITE FOR RESIDUE UEG D 300
08AC8SOFTWAREASN D:139 , LYS D:176 , GLY D:178 , SER D:186 , ASP D:188 , ASP D:202 , PHE D:204 , GLN D:205 , ASN D:209 , GLY D:211 , ALA D:212 , GLY D:213 , CYS D:214 , LYS D:238 , ILE D:245 , HOH D:2035 , HOH D:2036BINDING SITE FOR RESIDUE ACP D 500
09AC9SOFTWAREGLN C:205 , GLN C:206 , SER C:207 , THR D:274 , GLU D:275BINDING SITE FOR RESIDUE SO4 C1277
10BC1SOFTWAREGLN D:206 , SER D:207BINDING SITE FOR RESIDUE SO4 D1277
11BC2SOFTWAREGLY D:72 , ASN D:98 , HOH D:2019BINDING SITE FOR RESIDUE SO4 D1278
12BC3SOFTWARELEU D:30 , TYR D:223 , TYR D:263BINDING SITE FOR RESIDUE SO4 D1279
13BC4SOFTWAREGLY B:72 , ASN B:98 , HOH B:2038BINDING SITE FOR RESIDUE SO4 B1277
14BC5SOFTWARELYS A:185 , HIS B:172 , HOH B:2074BINDING SITE FOR RESIDUE SO4 B1278
15BC6SOFTWAREGLY C:72 , ASN C:98 , HOH C:2008BINDING SITE FOR RESIDUE SO4 C1278

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C5N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C5N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C5N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C5N)

(-) Exons   (0, 0)

(no "Exon" information available for 4C5N)

(-) 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4c5na_ A: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh.....hhhhhhhhhhhhhhh....eeee.hhhh...eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c5n A   1 GALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
                                    10        20        30        40        50        60        70        80        90       100       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268        
                                                                                                                                     108|                                                                                                                                                               
                                                                                                                                      117                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains d4c5nb_ B: automated matches                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhh.ee..hhhhhhhhh......hhhhhhhhhhhhhhh....eeee.hhhh...eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c5n B   1 GALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
                                    10        20        30        40        50        60        70        80        90       100       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267         
                                                                                                                                      109|                                                                                                                                                               
                                                                                                                                       117                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains d4c5nc_ C: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh.....hhhhhhhhhhhhhhh....eeeehhhhhh..eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c5n C   2 ALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
                                    11        21        31        41        51        61        71        81        91       101      |120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
                                                                                                                                    108|                                                                                                                                                              
                                                                                                                                     118                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains d4c5nd_ D: automated matches                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh.ee..hhhhhhhhhh.....hhhhhhhhhhhhhhh....eeee.hhhhh..eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c5n D   1 GALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVCNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
                                    10        20        30        40        50        60        70        80        90       100       110|      127       137       147       157       167       177       187       197       207       217       227       237       247       257       267         
                                                                                                                                       110|                                                                                                                                                              
                                                                                                                                        118
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  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)

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(no "CATH Domain" information available for 4C5N)

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(no "Pfam Domain" information available for 4C5N)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4c5j STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS
4c5k STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH ADP
4c5l STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH PYRIDOXAL
4c5m STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH AMP-PCP