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(-) Description

Title :  CRYSTAL STRUCTURE OF S. AUREUS HOMOSERINE DEHYDROGENASE AT PH7.0
 
Authors :  V. Navratna, B. Gopal
Date :  01 May 14  (Deposition) - 13 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: HOM, CH51_06975, JN533_07120, QT38_06630, SASCBU26_01217
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1ACT13Ligand/IonACETATE ION
2DMS3Ligand/IonDIMETHYL SULFOXIDE
3GOL3Ligand/IonGLYCEROL
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:242 , TYR A:244 , ASP A:269binding site for residue ACT A 501
02AC2SOFTWARELYS A:224 , GLU A:264binding site for residue ACT A 502
03AC3SOFTWAREVAL A:79 , GLY A:81 , ALA A:103 , ASN A:104 , LYS A:105binding site for residue ACT A 503
04AC4SOFTWAREASP A:181 , HOH A:653 , HIS B:382binding site for residue ACT A 504
05AC5SOFTWARELEU A:108 , LYS A:219 , LEU A:220 , HOH A:611 , HOH A:617binding site for residue ACT A 505
06AC6SOFTWAREGLN A:216 , VAL A:217 , GLY A:257 , VAL A:259binding site for residue ACT A 506
07AC7SOFTWAREASN A:237 , ASP A:240binding site for residue ACT A 507
08AC8SOFTWARELYS A:3 , ASN A:5 , SER A:72 , ASP A:74 , GLU B:416binding site for residue GOL A 508
09AC9SOFTWAREASP A:240 , HOH A:641 , ASP B:46 , SER B:48binding site for residue GOL A 509
10AD1SOFTWAREASN A:221 , VAL A:223 , ARG A:225binding site for residue PEG A 510
11AD2SOFTWAREGLY A:10 , LEU A:11 , ARG A:45 , MET A:80binding site for residue DMS A 511
12AD3SOFTWAREVAL B:79 , MET B:80 , GLY B:81 , ALA B:103 , ASN B:104 , LYS B:105 , PEG B:508binding site for residue ACT B 501
13AD4SOFTWARELYS A:412 , HIS A:413 , LYS B:376 , ALA B:377 , LEU B:379 , PHE B:381binding site for residue ACT B 502
14AD5SOFTWARELEU B:108 , VAL B:110 , LYS B:219 , LEU B:220 , HOH B:603 , HOH B:606binding site for residue ACT B 503
15AD6SOFTWAREARG B:26 , ILE B:39 , TYR B:58binding site for residue ACT B 504
16AD7SOFTWAREGLY B:230 , ASP B:418 , LYS B:419binding site for residue ACT B 505
17AD8SOFTWARELYS B:47 , ASP B:240 , GLN B:241 , GLY B:243 , LYS B:270binding site for residue ACT B 506
18AD9SOFTWARELYS B:47 , HIS B:59 , THR B:61 , GLU B:66 , THR B:170 , LYS B:171 , GLN B:173 , HOH B:641binding site for residue GOL B 507
19AE1SOFTWARELEU B:11 , GLY B:12 , VAL B:44 , ARG B:45 , ACT B:501binding site for residue PEG B 508
20AE2SOFTWAREHIS B:363 , VAL B:364 , LYS B:365 , HIS B:413 , GLY B:414 , TYR B:415 , HOH B:715binding site for residue PEG B 509
21AE3SOFTWARELEU B:242 , ARG B:386binding site for residue DMS B 510
22AE4SOFTWARELYS B:224 , ARG B:225 , ARG B:226 , GLU B:264binding site for residue DMS B 511

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PG6)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Glu A:84 -Pro A:85
2Asp A:289 -Ala A:290
3Leu B:53 -Asn B:54
4Glu B:84 -Pro B:85
5Ala B:130 -Ser B:131
6Pro B:137 -Ile B:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PG6)

(-) Exons   (0, 0)

(no "Exon" information available for 4PG6)

(-) 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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhheeeeeeeee..........hhhhh.ee.hhhhhhh.....eeee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh..eee....eeeeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhee......hhhhhhhhhhhheeeeeeeeeeee..eeeeeeeeeeee..hhhhhh...eeeeeeee.....eeeeee..hhhhhhhhhhhhhhhhh..........hhhhh....eeeeeeee....hhhhhhhhhhhhh....eeeeeeee..eeeeeeeee...hhhhhhhh..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pg6 A   0 HMKKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPLNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEANNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGDAVGDTMFYGKGAGSLATGSAVVSDLLNVALFFEPPHFELKTDKTREEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGV 426
                                     9        19        29        39        49        59        69        79        89        99       109       119       129||     157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317    || 333       354       364       374       384       394       404       414       424  
                                                                                                                                                            130|                                                                                                                                                                          322|         341|                                                                         
                                                                                                                                                             149                                                                                                                                                                           329          353                                                                         


Chain B from PDB  Type:PROTEIN  Length:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee................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
                 4pg6 B   1 MKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPLNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEASVAGIPINNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGAVGDTMFYGKGAGSLATGSAVVSDLLNVALFFEPPHFELKEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGVL 427
                            ||      11        21        31        41        51        61        71        81        91       101       111       121       131 ||  ||152       162       172       182       192       202       212       222       232       242       252       262       272       282     ||293       303       313       329     ||356       366       376       386       396       406       416       426 
                            1|                                                                                                                               133|  ||                                                                                                                                        288|                             322|   335|                                                                          
                             3                                                                                                                                135  ||                                                                                                                                         290                              329    353                                                                          
                                                                                                                                                                 138|                                                                                                                                                                                                                                                              
                                                                                                                                                                  149
   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 4PG6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PG6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PG6)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Leu B:53 - Asn B:54   [ RasMol ]  
    Pro B:137 - Ile B:138   [ RasMol ]  
 

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4pg4 4pg5 4pg7 4pg8