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(-) Description

Title :  THE CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE REDUCTASE FROM STAPHYLOCOCCUS AUREUS
 
Authors :  T. S. Girish, B. Gopal
Date :  03 Mar 11  (Deposition) - 03 Aug 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rossmann Fold, Reductase, Nadh, Nadph, Dihydrodipicolinate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Girish, V. Navratna, B. Gopal
Structure And Nucleotide Specificity Of Staphylococcus Aureus Dihydrodipicolinate Reductase (Dapb)
Febs Lett. V. 585 2561 2011
PubMed-ID: 21803042  |  Reference-DOI: 10.1016/J.FEBSLET.2011.07.021

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.3.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPB
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93062
    Strain: COL
    Synonym: DHPR

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric/Biological Unit (3, 26)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3SO422Ligand/IonSULFATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:136 , LYS A:213 , SO4 A:243 , HOH A:273 , HOH A:423BINDING SITE FOR RESIDUE SO4 A 241
02AC2SOFTWARELYS A:139 , SER A:144 , GLY A:145 , THR A:146 , HOH A:268 , HOH A:308 , HOH A:505 , HOH A:699BINDING SITE FOR RESIDUE SO4 A 242
03AC3SOFTWARELYS A:139 , VAL A:140 , ASP A:141 , SO4 A:241 , HOH A:423 , HOH A:601BINDING SITE FOR RESIDUE SO4 A 243
04AC4SOFTWAREALA A:10 , ARG A:14 , LYS A:213 , HOH A:508BINDING SITE FOR RESIDUE SO4 A 244
05AC5SOFTWAREARG A:14 , SER A:212 , LYS A:213 , HOH A:269 , HOH A:590BINDING SITE FOR RESIDUE GOL A 245
06AC6SOFTWARELYS B:138 , LYS B:139 , VAL B:140 , ASP B:141 , SO4 B:245 , HOH B:279 , HOH D:303 , HOH D:304BINDING SITE FOR RESIDUE ACT B 241
07AC7SOFTWAREARG B:14 , HOH B:257 , HOH B:259 , HOH C:284BINDING SITE FOR RESIDUE SO4 B 242
08AC8SOFTWAREALA B:10 , ARG B:14 , LYS B:213 , HOH B:304 , HOH B:305BINDING SITE FOR RESIDUE SO4 B 243
09AC9SOFTWAREVAL B:164 , TYR B:165 , ASP B:166 , LEU B:170 , HOH B:478BINDING SITE FOR RESIDUE SO4 B 244
10BC1SOFTWAREHIS B:136 , LYS B:139 , LYS B:213 , ACT B:241 , HOH B:275 , HOH B:279BINDING SITE FOR RESIDUE SO4 B 245
11BC2SOFTWARESER B:103 , ALA B:104 , ASN B:105 , HIS B:111 , LYS B:149 , PHE B:237 , HOH B:341 , HOH B:351 , HOH B:443BINDING SITE FOR RESIDUE SO4 B 246
12BC3SOFTWARETHR B:162 , GLN B:177 , HOH B:283BINDING SITE FOR RESIDUE SO4 B 247
13BC4SOFTWAREHOH B:257 , ARG C:14 , SER C:212 , HOH C:260 , HOH C:262 , HOH C:284 , HOH C:542BINDING SITE FOR RESIDUE SO4 C 241
14BC5SOFTWARETHR B:81 , LYS B:139 , SER B:144 , GLY B:145 , THR B:146 , HOH B:277BINDING SITE FOR RESIDUE GOL B 248
15BC6SOFTWARELYS C:139 , SER C:144 , GLY C:145 , THR C:146 , HOH C:310 , HOH C:486BINDING SITE FOR RESIDUE SO4 C 242
16BC7SOFTWARELYS C:139 , VAL C:140 , ASP C:141 , SO4 C:244 , HOH C:339 , HOH C:598BINDING SITE FOR RESIDUE SO4 C 243
17BC8SOFTWAREHIS C:136 , LYS C:213 , SO4 C:243 , HOH C:313 , HOH C:339 , HOH C:688BINDING SITE FOR RESIDUE SO4 C 244
18BC9SOFTWAREARG C:14 , LYS C:213 , HOH C:330 , HOH C:627BINDING SITE FOR RESIDUE SO4 C 245
19CC1SOFTWAREGLY C:9 , ALA C:10 , HOH C:338BINDING SITE FOR RESIDUE SO4 C 246
20CC2SOFTWARESER D:59 , ASN D:60 , PRO D:61 , THR D:80 , HOH D:321BINDING SITE FOR RESIDUE ACT D 241
21CC3SOFTWARELYS D:139 , SER D:144 , GLY D:145 , THR D:146 , HOH D:257 , HOH D:300BINDING SITE FOR RESIDUE SO4 D 242
22CC4SOFTWAREHIS D:136 , LYS D:139 , LYS D:213 , SO4 D:245 , HOH D:316 , HOH D:502BINDING SITE FOR RESIDUE SO4 D 243
23CC5SOFTWAREARG D:14 , LYS D:213 , HOH D:342 , HOH D:343BINDING SITE FOR RESIDUE SO4 D 244
24CC6SOFTWARELYS D:139 , VAL D:140 , ASP D:141 , SO4 D:243 , HOH D:502BINDING SITE FOR RESIDUE SO4 D 245
25CC7SOFTWAREGLY D:9 , ALA D:10 , HOH D:348BINDING SITE FOR RESIDUE SO4 D 246
26CC8SOFTWAREARG B:226 , LYS B:230 , ASN D:97 , ASN D:232 , HOH D:271 , HOH D:621 , HOH D:689BINDING SITE FOR RESIDUE SO4 D 247

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QY9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:142 -Pro A:143
2Ala B:142 -Pro B:143
3Ala C:142 -Pro C:143
4Ala D:142 -Pro D:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QY9)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAPBPS01298 Dihydrodipicolinate reductase signature.DAPB_STAAC130-147
 
 
 		  4A:130-147
B:130-147
C:130-147
D:130-147

(-) Exons   (0, 0)

(no "Exon" information available for 3QY9)

(-) Sequences/Alignments

Asymmetric/Biological 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:239
 aligned with DAPB_STAAC | Q5HG24 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:241
                             1                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
           DAPB_STAAC     - -MKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPKATTPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee.....--................eeee..hhhhhhhhhh......eee....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhh...eee.............eeeeeeee.....eeeeeeee...eeeeeeeee..hhhhhhhhhhhhhhhh....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------DAPB              --------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qy9 A   0 SMKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPK--TPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL 240
                                     9        19        29     |  39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
                                                              35 38                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with DAPB_STAAC | Q5HG24 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:241
                             1                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
           DAPB_STAAC     - -MKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPKATTPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee..............hhhhh....eeeee.hhhhhhhhhh......eeee....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhh...eee.hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeee..hhhhhhhhhhhhhhhh....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------DAPB              --------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qy9 B   0 SMKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPKATTPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL 240
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 


Chain C from PDB  Type:PROTEIN  Length:241
 aligned with DAPB_STAAC | Q5HG24 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:241
                             1                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
           DAPB_STAAC     - -MKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPKATTPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee...........ee.hhhhh....eeeee.hhhhhhhhhh......eeee....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhh...eee.............eeeeeeee.....eeeeeeee...eeeeeeeee..hhhhhhhhhhhhhhhh....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------DAPB              --------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qy9 C   0 SMKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPKATTPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL 240
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 


Chain D from PDB  Type:PROTEIN  Length:241
 aligned with DAPB_STAAC | Q5HG24 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:241
                             1                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
           DAPB_STAAC     - -MKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPKATTPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee...........ee.hhhhh....eeeee.hhhhhhhhhh......eeee....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhh...eee.............eeeeeeee.....eeeeeeee...eeeeeeeee..hhhhhhhhhhhhhhhh....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------DAPB              --------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qy9 D   0 SMKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPKATTPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL 240
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
   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 3QY9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QY9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QY9)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DAPB_STAAC | Q5HG24)
molecular function
    GO:0008839    4-hydroxy-tetrahydrodipicolinate reductase    Catalysis of the reaction: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016726    oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019877    diaminopimelate biosynthetic process    The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3qy9
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