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(-) Description

Title :  1.95 ANGSTROM CRYSTAL STRUCTURE OF OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM CLOSTRIDIUM DIFFICILE WITH COVALENT MODIFIED COMENIC ACID.
 
Authors :  G. Minasov, S. H. Light, L. Shuvalova, M-E. Duban, I. Dubrovska, J. Wins L. Papazisi, W. F. Anderson, Center For Structural Genomics Of I Diseases (Csgid)
Date :  13 Sep 12  (Deposition) - 26 Sep 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Tim Barrel, Aldolase Class I, 3-Dehydroquinate Dehydratase Activity, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, S. H. Light, L. Shuvalova, M-E. Duban, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 95 Angstrom Crystal Structure Of Of Type I 3-Dehydroquinate Dehydratase (Arod) From Clostridium Difficile With Covalent Modified Comenic Acid.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    Chains: A, B, C, D
    EC Number: 4.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19C
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: TYPE I 3-DEHYDROQUINATE DEHYDRATASE (AROD)
    Gene: AROD, CD630_22170
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Strain: 630
    Synonym: 3-DEHYDROQUINASE, TYPE I DHQASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE2Ligand/IonTRIETHYLENE GLYCOL
4SHL4Ligand/Ion5-HYDROXY-6-METHYL-4-OXO-4H-PYRAN-2-CARBOXYLIC ACID
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4SHL2Ligand/Ion5-HYDROXY-6-METHYL-4-OXO-4H-PYRAN-2-CARBOXYLIC ACID
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4SHL2Ligand/Ion5-HYDROXY-6-METHYL-4-OXO-4H-PYRAN-2-CARBOXYLIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:88 , PHE A:146 , HOH A:606BINDING SITE FOR RESIDUE PGE A 301
02AC2SOFTWAREILE A:24 , ARG A:49 , GLN A:237 , HOH A:602 , HOH A:623BINDING SITE FOR RESIDUE PEG A 302
03AC3SOFTWAREARG A:83 , HIS A:144 , LYS A:171 , MET A:204 , ARG A:214 , PHE A:226 , GLN A:237 , HOH A:592 , HOH A:594 , HOH A:595 , HOH A:602BINDING SITE FOR RESIDUE SHL A 303
04AC4SOFTWAREVAL B:86 , GLY B:88 , HOH B:521BINDING SITE FOR RESIDUE PEG B 301
05AC5SOFTWAREARG B:83 , HIS B:144 , LYS B:171 , MET B:204 , ARG B:214 , PHE B:226 , GLN B:237 , HOH B:450 , HOH B:574BINDING SITE FOR RESIDUE SHL B 302
06AC6SOFTWAREASP B:145 , PHE B:146 , ASN B:147BINDING SITE FOR RESIDUE ACT B 303
07AC7SOFTWAREPHE C:146 , HOH C:538 , HOH C:611BINDING SITE FOR RESIDUE PGE C 301
08AC8SOFTWAREARG C:83 , HIS C:144 , LYS C:171 , MET C:204 , ARG C:214 , PHE C:226 , GLN C:237 , HOH C:515 , HOH C:516BINDING SITE FOR RESIDUE SHL C 302
09AC9SOFTWAREARG D:83 , HIS D:144 , LYS D:171 , MET D:204 , ARG D:214 , PHE D:226 , GLN D:237 , HOH D:437 , HOH D:486 , HOH D:525 , HOH D:537BINDING SITE FOR RESIDUE SHL D 301
10BC1SOFTWAREGLU D:87 , PHE D:119 , ASN D:143BINDING SITE FOR RESIDUE ACT D 302
11BC2SOFTWAREPHE D:146 , ASN D:147 , HOH D:461 , HOH D:551BINDING SITE FOR RESIDUE ACT D 303

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:42 -D:42
2B:42 -C:42

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala B:234 -Pro B:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H3D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H3D)

(-) Exons   (0, 0)

(no "Exon" information available for 4H3D)

(-) Sequences/Alignments

Asymmetric 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:252
                                                                                                                                                                                                                                                                                            
               SCOP domains d4h3da_ A: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee..hhhhh.....hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h3d A   1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKAPGQISFKELNSVLNLLHKSIN 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230|      243       253  
                                                                                                                                                                                                                                                               230|                     
                                                                                                                                                                                                                                                                234                     


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains d4h3db_ B: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h3d B   1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKELNSVLNLLHKSI 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    


Chain C from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains d4h3dc_ C: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee..hhhhh.....hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h3d C   1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKAPGQISFKELNSVLNLLHKSIN 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230|      243       253  
                                                                                                                                                                                                                                                               230|                     
                                                                                                                                                                                                                                                                234                     


Chain D from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains d4h3dd_ D: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h3d D   0 AMKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSAPGQISFKELNSVLNLLHKSI 254
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 ||    241       251   
                                                                                                                                                                                                                                                                 231|                    
                                                                                                                                                                                                                                                                  234
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H3D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H3D)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  AROD_PEPD6 | Q186A6
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 Related Entries

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        AROD_PEPD6 | Q186A6: 3js3

(-) Related Entries Specified in the PDB File

3js3 CRYSTAL STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM CLOSTRIDIUM DIFFICILE WITH COVALENT REACTION INTERMEDIATE. RELATED ID: IDP90163 RELATED DB: TARGETTRACK