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(-) Description

Title :  CRYSTAL STRUCTURE OF S. AUREUS HOMOSERINE DEHYDROGENASE AT PH6.0
 
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, 25)

Asymmetric/Biological Unit (4, 25)
No.NameCountTypeFull Name
1ACT17Ligand/IonACETATE ION
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3GOL3Ligand/IonGLYCEROL
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:79 , MET A:80 , GLY A:81 , ALA A:103 , LYS A:105binding site for residue ACT A 501
02AC2SOFTWARELEU A:242 , TYR A:244 , ASP A:269binding site for residue ACT A 502
03AC3SOFTWAREARG A:226 , GLU A:264binding site for residue ACT A 503
04AC4SOFTWAREGLY A:10 , LEU A:11 , VAL A:44 , ARG A:45binding site for residue ACT A 504
05AC5SOFTWAREASP A:181 , HIS B:382binding site for residue ACT A 505
06AC6SOFTWAREGLN A:216 , VAL A:217 , GLY A:257 , VAL A:259binding site for residue ACT A 506
07AC7SOFTWAREVAL A:223 , LYS A:224 , ARG A:225binding site for residue ACT A 507
08AC8SOFTWARELEU A:108 , LYS A:219 , LEU A:220 , HOH A:647 , HOH A:665binding site for residue ACT A 508
09AC9SOFTWAREASN A:69 , HIS A:382 , ARG A:383binding site for residue ACT A 509
10AD1SOFTWARETYR A:281 , TYR A:297 , HOH A:612 , TYR B:285binding site for residue ACT A 510
11AD2SOFTWARELYS A:3 , ASN A:5 , SER A:72 , ASP A:74 , GLU B:416binding site for residue GOL A 511
12AD3SOFTWAREGLU A:190 , ASP A:192 , PRO A:193 , THR A:194 , ASP A:195 , ASP A:196binding site for residue PEG A 512
13AD4SOFTWAREGLY A:230 , ASP A:418 , LYS A:419binding site for residue PEG A 513
14AD5SOFTWARELYS A:412 , HIS A:413 , LYS B:376 , ALA B:377 , LEU B:379 , PHE B:381binding site for residue ACT B 501
15AD6SOFTWAREHIS B:413 , GLY B:414binding site for residue ACT B 502
16AD7SOFTWAREASP B:240 , GLN B:241 , GLY B:243 , LYS B:270binding site for residue ACT B 503
17AD8SOFTWARETYR B:244 , ARG B:386 , VAL B:398 , VAL B:400binding site for residue ACT B 504
18AD9SOFTWAREARG B:26 , ILE B:39 , TYR B:58binding site for residue ACT B 505
19AE1SOFTWAREARG B:226 , LYS B:419 , GOL B:508 , HOH B:621binding site for residue ACT B 506
20AE2SOFTWARELEU B:108 , LYS B:219 , LEU B:220 , HOH B:601 , HOH B:652binding site for residue ACT B 507
21AE3SOFTWAREGLN A:30 , GLY B:230 , ASP B:418 , LYS B:419 , ACT B:506binding site for residue GOL B 508
22AE4SOFTWAREASP A:240 , LYS A:270 , ASP B:46binding site for residue GOL B 509
23AE5SOFTWARELYS B:47 , HIS B:59 , LEU B:60 , THR B:61 , GLU B:66 , THR B:170 , LYS B:171binding site for residue PEG B 510
24AE6SOFTWAREVAL B:79 , MET B:80 , GLY B:81 , ALA B:103 , LYS B:105binding site for residue DMS B 511
25AE7SOFTWARELEU B:242 , TYR B:244 , ASP B:269 , ARG B:386binding site for residue DMS B 512

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PG4)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Glu A:84 -Pro A:85
2Arg B:51 -Pro B:52
3Glu B:84 -Pro B:85
4Gly B:134 -Gly B:135
5Pro B:137 -Ile B:138
6Asn B:149 -Asn B:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PG4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PG4)

(-) Exons   (0, 0)

(no "Exon" information available for 4PG4)

(-) 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:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhheeeeeeeee........hhhhhh..ee.hhhhhhh.....eeee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eee....eeeeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhee......hhhhhhhhhhhheeeeeeeeeeee..eeeeeeeeeeee..hhhhhh....eeeeeee.....eeeee...hhhhhhhhhhhhhhhhhhhh.................eeeeeeee....hhhhhhhhhhhhh....eeeeeeee..eeeeeeeee...hhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pg4 A   0 HMKKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPLNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEANNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGDAVGDTMFYGKGAGSLATGSAVVSDLLNVALFFETLPPHFELKTDKIKEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGVL 427
                                     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    || 331      |353       363       373       383       393       403       413       423    
                                                                                                                                                            130|                                                                                                                                                                          322|        338|                                                                            
                                                                                                                                                             149                                                                                                                                                                           327         351                                                                            


Chain B from PDB  Type:PROTEIN  Length:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhheeeeeeeee...............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
                 4pg4 B   1 MKKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEASVAGGIPIVNNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGVGDTMFYGKGAGSLATGSAVVSDLLNVALFEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGVL 427
                                    10        20        30        40        50 ||     61        71        81        91       101       111       121       131       150       160       170       180       190       200       210       220       230       240       250       260       270       280       292       302       312       354       364       374       384       394       404       414       424   
                                                                              52|                                                                                  139|                                                                                                                                        288|                          320|                                                                          
                                                                               54                                                                                   149                                                                                                                                         291                           353
   Legend:   → Mismatch (orange background)
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    → 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 4PG4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PG4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PG4)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PG4)

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  Cis Peptide Bonds
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    Pro B:137 - Ile B:138   [ RasMol ]  
 

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        A0A0M3KKV6_S | A0A0M3KKV6: 4pg5 4pg7 4pg8

(-) Related Entries Specified in the PDB File

4pg5 4pg6 4pg7 4pg8