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(-) Description

Title :  CRYSTAL STRUCTURE OF S. AUREUS HOMOSERINE DEHYDROGENASE AT PH7.5
 
Authors :  V. Navratna, B. Gopal
Date :  01 May 14  (Deposition) - 06 May 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
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, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1ACT11Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3LYS1Mod. Amino AcidLYSINE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
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
02AC2SOFTWAREASP A:181 , HOH A:612binding site for residue ACT A 502
03AC3SOFTWARETYR A:281 , TYR A:297 , HOH A:752 , TYR B:285binding site for residue ACT A 503
04AC4SOFTWARELEU A:242 , TYR A:244 , ASP A:269binding site for residue ACT A 504
05AC5SOFTWAREARG A:225 , GLU A:264binding site for residue ACT A 505
06AC6SOFTWAREASP A:240 , LYS A:270 , ASP B:46 , GLU B:62binding site for residue GOL A 506
07AC7SOFTWARELYS A:3 , ASN A:5 , SER A:72 , ASP A:74 , GLU B:416binding site for residue GOL A 507
08AC8SOFTWARELYS A:47 , HIS A:59 , LEU A:60 , THR A:61 , GLU A:66binding site for residue GOL A 508
09AC9SOFTWAREARG A:226 , GLY A:230 , ASP A:418 , LYS A:419 , HOH A:655binding site for residue LYS A 509
10AD1SOFTWAREVAL B:79 , MET B:80 , GLY B:81 , ALA B:103 , ASN B:104 , LYS B:105binding site for residue ACT B 501
11AD2SOFTWARELEU B:242 , TYR B:244 , ASP B:269 , ACT B:504 , HOH B:688binding site for residue ACT B 502
12AD3SOFTWAREASP B:240 , GLN B:241 , GLY B:243 , LYS B:270binding site for residue ACT B 503
13AD4SOFTWARETYR B:244 , ARG B:386 , VAL B:398 , VAL B:400 , ACT B:502 , HOH B:664 , HOH B:740binding site for residue ACT B 504
14AD5SOFTWAREHIS B:363 , GLY B:414 , TYR B:415 , HOH B:665 , HOH B:672binding site for residue PEG B 505
15AD6SOFTWARELYS B:113 , ASN B:215 , GLN B:216 , VAL B:217 , HOH B:751binding site for residue PEG B 506
16AD7SOFTWARELYS A:412 , HIS A:413 , HOH A:613 , ALA B:377 , LEU B:379 , PHE B:381binding site for residue ACT B 507
17AD8SOFTWAREARG B:26 , ILE B:39 , TYR B:58binding site for residue ACT B 508
18AD9SOFTWARELYS B:47 , HIS B:59 , LEU B:60 , THR B:61 , GLU B:66 , THR B:170 , LYS B:171 , ASP B:240 , HOH B:601 , HOH B:696binding site for residue GOL B 509

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PG7)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Glu A:84 -Pro A:85
2Asp A:289 -Ala A:290
3Ala A:301 -Gly A:302
4Glu B:84 -Pro B:85
5Ala B:301 -Gly B:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PG7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PG7)

(-) Exons   (0, 0)

(no "Exon" information available for 4PG7)

(-) 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:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhheeeeeeeee..........hhhhh.ee.hhhhhhh.....eeee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eehhhhh......eeeeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhee......hhhhhhhhhhhheeeeeeeeeeee..eeeeeeeeeeee..hhhhhh....eeeeeee.....eeeee...hhhhhhhhhhhhhhhhhhh.............hhhhhh..eeeeeeee....hhhhhhhhhhhhh....eeeeeeee..eeeeeeeee...hhhhhhhh..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pg7 A   0 HMKKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPLNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEASVAGGPNNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGDAVGDTMFYGKGAGSLATGSAVVSDLLNVALFFESTLPPHFELKTDKTREMEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGV 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 ||    334       354       364       374       384       394       404       414       424  
                                                                                                                                                                 135||                                                                                                                                                                           323|            342|                                                                         
                                                                                                                                                                  137|                                                                                                                                                                            327             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 .eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee................ee.hhhhhhh.....eeee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eehhhhh.......eeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhee......hhhhhhhhhhhheeeeeeeeeeee..eeeeeeeeeeee..hhhhhh....eeeeee.....eeeee...hhhhhhhhhhhhhhhhhh...........eeeeeeee....hhhhhhhhhhhhh....eeeeeeee..eeeeeeeee...hhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pg7 B   2 KKLNIALLGLGTVGSGVVKIIEENRQQIQDTLNKDIVIKHILVRDKSKKRPLNISQYHLTEDVNEILNDDSLDIIVEVMGGIEPTVDWLRTALKNKKHVITANKDLLAVHLKLLEDLAEENGVALKFEASVAGPNNISKFMGILNGTSNFILSKMTKEQTTFEEALDEAKRLGFAEADPTDDVEGVDAARKVVITSYLSFNQVIKLNDVKRRGISGVTLTDINVADQLGYKIKLIGKGIYENGKVNASVEPTLIDKKHQLAAVEDEYNAIYVIGAVGDTMFYGKGAGSLATGSAVVSDLLNVALFHTPPHFELEKSNFFVVVNHVKGSIENFENELKAILPFHRSLRVANYDNQSYAAVIVGLESSPEELITKHGYEVDKVYPVEGVL 427
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  |||  154       164       174       184       194       204       214       224       234       244       254       264       274       284   ||  295       305       315    |||331  ||   359       369       379       389       399       409       419        
                                                                                                                                                              134||                                                                                                                                        288|                           320|||  334|                                                                          
                                                                                                                                                               137|                                                                                                                                         290                            326||   353                                                                          
                                                                                                                                                                149                                                                                                                                                                         327|                                                                                
                                                                                                                                                                                                                                                                                                                                             329
   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 4PG7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PG7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PG7)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PG7)

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  Cis Peptide Bonds
    Ala A:301 - Gly A:302   [ RasMol ]  
    Ala B:301 - Gly B:302   [ RasMol ]  
    Asp A:289 - Ala A:290   [ RasMol ]  
    Glu A:84 - Pro A:85   [ RasMol ]  
    Glu B:84 - Pro B:85   [ RasMol ]  
 

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  A0A0M3KKV6_S | A0A0M3KKV6
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        A0A0M3KKV6_S | A0A0M3KKV6: 4pg4 4pg5 4pg8

(-) Related Entries Specified in the PDB File

4pg4 4pg5 4pg6 4pg8