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(-) Description

Title :  CRYSTAL STRUCTURE OF S. AUREUS HOMOSERINE DEHYDROGENASE AT PH8.5
 
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, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
1ACT16Ligand/IonACETATE ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3GOL1Ligand/IonGLYCEROL
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:242 , TYR A:244 , ASP A:269binding site for residue ACT A 501
02AC2SOFTWAREVAL A:79 , MET A:80 , GLY A:81 , ALA A:103 , ASN A:104 , LYS A:105binding site for residue ACT A 502
03AC3SOFTWAREGLU A:264binding site for residue ACT A 503
04AC4SOFTWAREHIS A:382 , ARG A:383 , SER A:384 , HOH A:601 , HOH A:617binding site for residue ACT A 504
05AC5SOFTWAREGLY A:10 , LEU A:11 , ARG A:45 , ARG A:51binding site for residue ACT A 505
06AC6SOFTWARETYR A:281 , TYR A:297 , HOH A:714 , TYR B:285 , HOH B:647binding site for residue ACT A 506
07AC7SOFTWAREASN A:5 , SER A:72 , ASP A:74 , GLU B:416binding site for residue ACT A 507
08AC8SOFTWAREGLN A:216 , VAL A:217 , GLY A:257 , VAL A:259binding site for residue ACT A 508
09AC9SOFTWARETHR A:170 , ASN A:237 , ASP A:240 , HOH A:618 , PEG B:510binding site for residue ACT A 509
10AD1SOFTWAREASN A:221 , VAL A:223 , LYS A:224 , ARG A:225binding site for residue PEG A 510
11AD2SOFTWAREVAL B:79 , MET B:80 , GLY B:81 , ALA B:103 , ASN B:104 , LYS B:105binding site for residue ACT B 501
12AD3SOFTWAREHIS A:413 , ALA B:377 , LEU B:379binding site for residue ACT B 502
13AD4SOFTWAREGLN B:216 , VAL B:217 , GLY B:257 , VAL B:259binding site for residue ACT B 503
14AD5SOFTWARELYS B:224 , GLU B:264binding site for residue ACT B 504
15AD6SOFTWAREASP B:240 , GLN B:241 , GLY B:243 , LYS B:270binding site for residue ACT B 505
16AD7SOFTWAREHIS B:413 , GLY B:414binding site for residue ACT B 506
17AD8SOFTWARELYS B:113 , GLU B:116 , ASP B:117 , TYR B:211 , ASN B:215binding site for residue ACT B 507
18AD9SOFTWAREHIS B:59 , THR B:61 , GLU B:66 , THR B:170 , LYS B:171 , GLN B:173 , HOH B:612 , HOH B:693binding site for residue GOL B 508
19AE1SOFTWARELEU B:11 , ARG B:45 , ASP B:46 , ARG B:51 , MET B:80binding site for residue PEG B 509
20AE2SOFTWAREASP A:240 , LYS A:270 , ACT A:509 , ASP B:46 , HOH B:625binding site for residue PEG B 510
21AE3SOFTWARELEU B:242 , ASP B:269 , ARG B:386 , HOH B:661binding site for residue DMS B 511

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PG8)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Glu A:84 -Pro A:85
2Asp A:289 -Ala A:290
3Leu A:334 -Lys A:335
4Lys A:335 -Thr A:336
5Glu B:84 -Pro B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PG8)

(-) Exons   (0, 0)

(no "Exon" information available for 4PG8)

(-) 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:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhheeeeeeeee..........hhhhh.ee.hhhhhhh.....eeee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eehhhhhh.....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
                 4pg8 A   0 HMKKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPLNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEASVAGGPNNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGDAVGDTMFYGKGAGSLATGSAVVSDLLNVALFFELPPHFELKTDKTREEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGV 426
                                     9        19        29        39        49        59        69        79        89        99       109       119       129     ||151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321||     336    || 357       367       377       387       397       407       417         
                                                                                                                                                                 135||                                                                                                                                                                          322|          341|                                                                         
                                                                                                                                                                  137|                                                                                                                                                                           328           353                                                                         
                                                                                                                                                                   149                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhh.hhhhhhhhhhh.eeeeeeeee................ee.hhhhhhh.....eeee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eee.............eeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhee......hhhhhhhhhhhheeeeeeeeeeee..eeeeeeeeeeee..hhhhhh....eeeeee....eeeee...hhhhhhhhhhhhhhhhhhh........eeeeeeee....hhhhhhhhhhhhh....eeeeeeee..eeeeeeeee...hhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pg8 B   1 MKKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPLNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEASVAIPIVNNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGVGDTMFYGKGAGSLATGSAVVSDLLNVALFFPHFELEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGVL 427
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   151       161       171       181       191       201       211       221       231       241       251       261       271       281      |293       303       313       331  ||   359       369       379       389       399       409       419        
                                                                                                                                                              133| 140|                                                                                                                                       288|                           321| 334|                                                                          
                                                                                                                                                               136  150                                                                                                                                        291                            330  353
   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 4PG8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PG8)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PG8)

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  Cis Peptide Bonds
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 Related Entries

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        A0A0M3KKV6_S | A0A0M3KKV6: 4pg4 4pg5 4pg7

(-) Related Entries Specified in the PDB File

4pg4 4pg5 4pg6 4pg7