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(-) Description

Title :  CRYSTAL STRUCTURE OF S. AUREUS HOMOSERINE DEHYDROGENASE AT PH6.5
 
Authors :  V. Navratna, B. Gopal
Date :  01 May 14  (Deposition) - 06 May 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aspartic Acid Pathway, Ph Sensitivity, Hydride Transfer, Act Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Navratna, G. Reddy, B. Gopal
Structural Basis For The Catalytic Mechanism Of Homoserine Dehydrogenase.
Acta Crystallogr. , Sect. D V. 71 1216 2015
PubMed-ID: 25945586  |  Reference-DOI: 10.1107/S1399004715004617

(-) Compounds

Molecule 1 - HOMOSERINE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: U5K_01898
    Organism Scientific: STAPHYLOCOCCUS AUREUS M1064
    Organism Taxid: 1158465
    Synonym: HDH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1ACT11Ligand/IonACETATE ION
2DMS4Ligand/IonDIMETHYL SULFOXIDE
3GOL2Ligand/IonGLYCEROL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:79 , MET A:80 , GLY A:81 , ALA A:103 , ASN A:104 , LYS A:105binding site for residue ACT A 501
02AC2SOFTWARELEU A:242 , TYR A:244 , ASP A:269 , ARG A:386 , HOH A:661binding site for residue ACT A 502
03AC3SOFTWAREGLN A:216 , VAL A:217 , GLY A:257 , VAL A:259binding site for residue ACT A 503
04AC4SOFTWAREGLU A:264binding site for residue ACT A 504
05AC5SOFTWARETHR A:170 , ASN A:237 , ASP A:240binding site for residue ACT A 505
06AC6SOFTWARETYR A:281 , TYR A:297 , HOH A:682 , TYR B:285binding site for residue ACT A 506
07AC7SOFTWAREHIS A:363 , LYS A:365 , GLY A:414 , HOH A:607binding site for residue ACT A 507
08AC8SOFTWAREASP A:240 , ASP B:46 , SER B:48binding site for residue GOL A 508
09AC9SOFTWAREASN A:221 , VAL A:223 , ARG A:225binding site for residue PEG A 509
10AD1SOFTWAREGLN B:216 , VAL B:217 , ILE B:218 , GLY B:257 , LYS B:258 , VAL B:259binding site for residue ACT B 501
11AD2SOFTWARELYS B:224 , ARG B:226 , GLU B:264binding site for residue ACT B 502
12AD3SOFTWARETYR B:244 , ARG B:386 , VAL B:398 , DMS B:510 , HOH B:619binding site for residue ACT B 503
13AD4SOFTWARELEU B:108 , LYS B:219 , LEU B:220 , HOH B:603 , HOH B:604binding site for residue ACT B 504
14AD5SOFTWAREHIS A:413 , GLY A:414 , HOH A:672 , LYS B:376 , ALA B:377 , LEU B:379 , PHE B:381binding site for residue DMS B 505
15AD6SOFTWAREVAL B:79 , MET B:80 , GLY B:81 , ALA B:103 , ASN B:104 , LYS B:105binding site for residue DMS B 506
16AD7SOFTWAREHIS B:413 , GLY B:414 , TYR B:415binding site for residue DMS B 507
17AD8SOFTWAREVAL B:38 , ILE B:39 , GLN B:57 , TYR B:58 , HOH B:635binding site for residue GOL B 508
18AD9SOFTWAREGLY B:230 , THR B:232 , ASP B:418 , LYS B:419binding site for residue PEG B 509
19AE1SOFTWARELEU B:242 , ASP B:269 , ARG B:386 , ACT B:503binding site for residue DMS B 510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PG5)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:84 -Pro A:85
2Asp A:289 -Ala A:290
3Glu B:84 -Pro B:85
4Pro B:137 -Ile B:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PG5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PG5)

(-) Exons   (0, 0)

(no "Exon" information available for 4PG5)

(-) 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:395
                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhheeeeeeeee..........hhhhh.ee.hhhhhhh.....eeee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eee.......eeeeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhee......hhhhhhhhhhhheeeeeeeeeeee..eeeeeeeeeeee..hhhhhh...eeeeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhh.......hhhhh....eeeeeeee....hhhhhhhhhhhhh....eeeeeeee..eeeeeeeee...hhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pg5 A   0 HMKKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPLNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEAVGGNNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGDAVGDTMFYGKGAGSLATGSAVVSDLLNVALFFLHPPHFELKTDKTEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGVL 427
                                     9        19        29        39        49        59        69        79        89        99       109       119       129|||||  154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314      |329       339|      362       372       382       392       402       412       422     
                                                                                                                                                            130||||                                                                                                                                                                         321|||       339|                                                                          
                                                                                                                                                             132|||                                                                                                                                                                          325||        353                                                                          
                                                                                                                                                              134||                                                                                                                                                                           326|                                                                                     
                                                                                                                                                               135|                                                                                                                                                                            329                                                                                     
                                                                                                                                                                149                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:396
                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhhhh....eeeeeee...............ee.hhhhhhh.....eeee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eee............eeeeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhee......hhhhhhhhhhhheeeeeeeeeeee..eeeeeeeeeeee..hhhhhh....eeeeeee.....eeeee...hhhhhhhhhhhhhhhhhhh...............eeeeeeee....hhhhhhhhhhhhh....eeeeeeee..eeeeeeeee...hhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pg5 B   1 MKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEASVGGIPIVNNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGDAVGDTMFYGKGAGSLATGSAVVSDLLNVALFFLTLHFELKTDKTEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGVL 427
                            ||      11        21        31        41        51||      62        72        82        92       102       112       122       132|    ||152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       325|||    338||     361       371       381       391       401       411       421      
                            1|                                               52|                                                                           132|  139|                                                                                                                                                                         321||||     339|                                                                          
                             3                                                54                                                                            134   149                                                                                                                                                                          325|||      353                                                                          
                                                                                                                                                                                                                                                                                                                                                327||                                                                                   
                                                                                                                                                                                                                                                                                                                                                 328|                                                                                   
                                                                                                                                                                                                                                                                                                                                                  331
   Legend:   → Mismatch (orange background)
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  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 4PG5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PG5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PG5)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PG5)

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  Cis Peptide Bonds
    Asp A:289 - Ala A:290   [ RasMol ]  
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        A0A0M3KKV6_S | A0A0M3KKV6: 4pg4 4pg7 4pg8

(-) Related Entries Specified in the PDB File

4pg4 4pg6 4pg7 4pg8