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(-) Description

Title :  STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH AMP-PCP
 
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 :  1.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,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 SUBSP. AUREUS MU50
    Organism Taxid: 158878
    Synonym: PYRIDOXAL KINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1ACP4Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO417Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO49Ligand/IonSULFATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO48Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:139 , LYS A:176 , GLY A:178 , LYS A:179 , SER A:186 , ASP A:188 , ASP A:202 , MET A:203 , PHE A:204 , GLN A:205 , ASN A:209 , GLY A:213 , LYS A:238 , ILE A:245 , SO4 A:1280 , HOH A:2161 , HOH A:2162 , HOH A:2164 , HOH A:2165 , HOH A:2185 , HOH A:2194BINDING SITE FOR RESIDUE ACP A 500
02AC2SOFTWAREASN B:139 , LYS B:176 , GLY B:178 , LYS B:179 , SER B:186 , ASP B:188 , ASP B:202 , MET B:203 , PHE B:204 , GLN B:205 , ASN B:209 , GLY B:213 , LYS B:238 , ILE B:245 , HOH B:2151 , HOH B:2152 , HOH B:2154 , HOH B:2177 , HOH B:2181BINDING SITE FOR RESIDUE ACP B 500
03AC3SOFTWAREASN C:139 , LYS C:176 , LYS C:179 , SER C:186 , ASP C:188 , ASP C:202 , MET C:203 , PHE C:204 , GLN C:205 , ASN C:209 , GLY C:213 , LYS C:238 , ILE C:245 , HOH C:2102 , HOH C:2103 , HOH C:2131BINDING SITE FOR RESIDUE ACP C 500
04AC4SOFTWARELYS D:176 , GLY D:178 , LYS D:179 , SER D:186 , ASP D:188 , ASP D:202 , MET D:203 , PHE D:204 , GLN D:205 , ASN D:209 , GLY D:213 , LYS D:238 , ILE D:245 , SO4 D:1280 , HOH D:2128 , HOH D:2129 , HOH D:2152 , HOH D:2167BINDING SITE FOR RESIDUE ACP D 500
05AC5SOFTWAREGLN B:205 , GLN B:206 , SER B:207 , HOH B:2192 , HOH B:2247BINDING SITE FOR RESIDUE SO4 B1277
06AC6SOFTWARETYR B:208 , LYS B:250 , HOH B:2159 , HOH B:2160 , HOH B:2248BINDING SITE FOR RESIDUE SO4 B1278
07AC7SOFTWAREHOH A:2273 , GLN D:205 , GLN D:206 , SER D:207 , HOH D:2250BINDING SITE FOR RESIDUE SO4 D1277
08AC8SOFTWARETYR C:208 , LYS C:250 , HOH C:2199BINDING SITE FOR RESIDUE SO4 C1277
09AC9SOFTWAREGLN C:205 , GLN C:206 , SER C:207 , HOH C:2144BINDING SITE FOR RESIDUE SO4 C1278
10BC1SOFTWAREGLY A:72 , ASN A:98 , HOH A:2107BINDING SITE FOR RESIDUE SO4 A1277
11BC2SOFTWAREGLN A:205 , GLN A:206 , SER A:207BINDING SITE FOR RESIDUE SO4 A1278
12BC3SOFTWAREHIS A:210 , VAL A:255 , SO4 A:1280 , HOH A:2218BINDING SITE FOR RESIDUE SO4 A1279
13BC4SOFTWARETYR B:223 , LYS B:228 , TYR B:263 , HOH B:2205 , HOH B:2235 , HOH B:2249BINDING SITE FOR RESIDUE SO4 B1279
14BC5SOFTWARELYS B:5 , ASN B:98 , HOH B:2010 , HOH B:2097BINDING SITE FOR RESIDUE SO4 B1280
15BC6SOFTWARELYS D:5 , GLY D:72 , ASN D:98 , HOH D:2004 , HOH D:2073BINDING SITE FOR RESIDUE SO4 D1278
16BC7SOFTWAREPRO C:57 , MET C:58 , HOH C:2042BINDING SITE FOR RESIDUE SO4 C1279
17BC8SOFTWAREHIS A:268 , HOH A:2267 , THR D:83 , GLU D:84 , ASN D:121 , HOH D:2083BINDING SITE FOR RESIDUE SO4 D1279
18BC9SOFTWAREHIS D:210 , GLY D:211 , ALA D:212 , GLY D:213 , CYS D:214 , ACP D:500 , HOH D:2193 , HOH D:2252 , HOH D:2254BINDING SITE FOR RESIDUE SO4 D1280
19CC1SOFTWAREHIS A:210 , GLY A:211 , ALA A:212 , GLY A:213 , CYS A:214 , ACP A:500 , SO4 A:1279BINDING SITE FOR RESIDUE SO4 A1280
20CC2SOFTWARELYS D:185 , TYR D:187 , HOH D:2165 , HOH D:2179BINDING SITE FOR RESIDUE SO4 D1281
21CC3SOFTWAREGLY C:72 , ASN C:98 , HOH C:2009 , HOH C:2055BINDING SITE FOR RESIDUE SO4 C1280

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C5M)

(-) Exons   (0, 0)

(no "Exon" information available for 4C5M)

(-) 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:273
 aligned with A0A0H3JTP0_S | A0A0H3JTP0 from UniProtKB/TrEMBL  Length:276

    Alignment length:276
                                    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      
         A0A0H3JTP0_S     1 MALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVCKGEDEVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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....eeeehhhhhh..eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c5m A   1 GALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVCK---EVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
                                    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      
                                                                                                                                        111 115                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:276
 aligned with A0A0H3JTP0_S | A0A0H3JTP0 from UniProtKB/TrEMBL  Length:276

    Alignment length:276
                                    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      
         A0A0H3JTP0_S     1 MALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVCKGEDEVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee.....eee..ee.hhhhhhhhhhhhhhhh.ee..hhhhhhhhh......hhhhhhhhhhhhhhh....eeee.hhhh...eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c5m B   1 GALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVCKGEDEVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
                                    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      


Chain C from PDB  Type:PROTEIN  Length:273
 aligned with A0A0H3JTP0_S | A0A0H3JTP0 from UniProtKB/TrEMBL  Length:276

    Alignment length:276
                                    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      
         A0A0H3JTP0_S     1 MALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVCKGEDEVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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.hhhh...eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c5m C   1 GALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVC---DEVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
                                    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      
                                                                                                                                       110 114                                                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:273
 aligned with A0A0H3JTP0_S | A0A0H3JTP0 from UniProtKB/TrEMBL  Length:276

    Alignment length:276
                                    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      
         A0A0H3JTP0_S     1 MALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVCKGEDEVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee....ee.---.eehhhhhhhhhhhhhhhh.ee..hhhhhhhhhh.....hhhhhhhhhhhhhhh....eeeehhhhhh..eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c5m D   1 GALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVCK---EVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV 276
                                    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      
                                                                                                                                        111 115
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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  (0, 0)

(no "SCOP Domain" information available for 4C5M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C5M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C5M)

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 Related Entries

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

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        A0A0H3JTP0_S | A0A0H3JTP0: 4c5j 4c5k 4c5l

(-) 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
4c5n STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH AMP-PCP AND PYRIDOXAL