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(-) Description

Title :  1.65 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF TYPE II 3-DEHYDROQUINATE DEHYDRATASE (AROQ) FROM YERSINIA PESTIS
 
Authors :  G. Minasov, S. H. Light, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  24 Feb 10  (Deposition) - 09 Mar 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Type Ii 3-Dehydroquinate Dehydratase, Aroq, Idp90771, Amino- Acid Biosynthesis, Aromatic Amino Acid Biosynthesis, Lyase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, S. H. Light, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 65 Angstrom Resolution Crystal Structure Of Type Ii 3-Dehydroquinate Dehydratase (Aroq) From Yersinia Pestis.
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: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: 3-DEHYDROQUINATE DEHYDRATASE (AROQ)
    Gene: AROQ, Y0207, YPO3660, YP_3886
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: 3-DEHYDROQUINASE, TYPE II DHQASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric Unit (3, 22)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL17Ligand/IonGLYCEROL
Biological Unit 1 (3, 66)
No.NameCountTypeFull Name
1BME12Ligand/IonBETA-MERCAPTOETHANOL
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL51Ligand/IonGLYCEROL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:106 , VAL A:107 , HIS A:108 , CYS A:128 , GOL A:152 , BME D:151BINDING SITE FOR RESIDUE BME A 151
02AC2SOFTWAREHIS A:83 , GLU A:101 , HIS A:108 , ARG A:114 , HIS A:115 , HIS A:116 , SER A:117 , SER A:120 , VAL A:126 , BME A:151 , HIS D:108BINDING SITE FOR RESIDUE GOL A 152
03AC3SOFTWAREALA A:79 , HIS A:83 , SER A:105 , ARG A:110 , ARG A:114 , HOH A:164 , HOH A:305 , HOH A:641BINDING SITE FOR RESIDUE GOL A 153
04AC4SOFTWARELEU A:92 , GLN A:96 , ILE A:97 , PRO A:98 , PHE A:99 , HOH A:157 , HOH A:192 , HOH A:302 , HOH A:372 , HOH A:625BINDING SITE FOR RESIDUE GOL A 154
05AC5SOFTWARESER A:117 , TYR A:118 , ASP A:121 , HIS D:115BINDING SITE FOR RESIDUE GOL A 155
06AC6SOFTWAREGLU A:111 , HOH A:557 , HOH A:590 , ARG B:89 , HOH B:196BINDING SITE FOR RESIDUE GOL A 156
07AC7SOFTWAREASN B:106 , VAL B:107 , HIS B:108 , CYS B:128 , GOL B:153 , BME C:151BINDING SITE FOR RESIDUE BME B 151
08AC8SOFTWAREALA B:79 , HIS B:83 , SER B:105 , ARG B:110 , ARG B:114 , HOH B:244 , HOH B:497 , HOH B:505 , HOH B:566 , HOH B:643BINDING SITE FOR RESIDUE GOL B 152
09AC9SOFTWAREHIS B:83 , GLU B:101 , HIS B:103 , HIS B:108 , ARG B:114 , HIS B:115 , HIS B:116 , SER B:117 , SER B:120 , BME B:151 , HIS C:108BINDING SITE FOR RESIDUE GOL B 153
10BC1SOFTWARELEU B:92 , GLN B:96 , ILE B:97 , PHE B:99 , HOH B:155 , HOH B:515BINDING SITE FOR RESIDUE GOL B 154
11BC2SOFTWAREBME B:151 , ASN C:106 , VAL C:107 , VAL C:126 , CYS C:128 , GOL C:153BINDING SITE FOR RESIDUE BME C 151
12BC3SOFTWAREHOH A:634 , ALA C:79 , HIS C:83 , SER C:105 , ARG C:110 , ARG C:114 , HOH C:181 , HOH C:187BINDING SITE FOR RESIDUE GOL C 152
13BC4SOFTWAREHIS B:108 , HIS C:83 , GLU C:101 , HIS C:108 , ARG C:114 , HIS C:115 , HIS C:116 , SER C:117 , SER C:120 , BME C:151BINDING SITE FOR RESIDUE GOL C 153
14BC5SOFTWAREARG C:89 , HIS C:116 , SER C:117 , ASP C:121 , HOH C:220 , HOH C:667BINDING SITE FOR RESIDUE GOL C 154
15BC6SOFTWAREBME A:151 , ASN D:106 , VAL D:107 , HIS D:108 , CYS D:128BINDING SITE FOR RESIDUE BME D 151
16BC7SOFTWAREHIS D:51 , SER D:63 , HOH D:169 , HOH D:171 , HOH D:273BINDING SITE FOR RESIDUE EDO D 152
17BC8SOFTWAREALA D:79 , HIS D:83 , SER D:105 , ARG D:110 , ARG D:114 , HOH D:214 , HOH D:338 , HOH D:619 , HOH D:642BINDING SITE FOR RESIDUE GOL D 153
18BC9SOFTWAREARG D:89 , HIS D:116 , SER D:117 , TYR D:118 , ASP D:121 , HOH D:245BINDING SITE FOR RESIDUE GOL D 154
19CC1SOFTWAREHIS A:108 , HIS D:83 , GLU D:101 , HIS D:108 , ARG D:114 , HIS D:115 , HIS D:116 , SER D:117 , SER D:120BINDING SITE FOR RESIDUE GOL D 155
20CC2SOFTWAREARG D:110 , GLU D:111 , HOH D:601 , HOH D:640BINDING SITE FOR RESIDUE GOL D 156
21CC3SOFTWARELEU D:92 , GLN D:96 , ILE D:97 , PRO D:98 , PHE D:99 , HOH D:160 , HOH D:322 , HOH D:655BINDING SITE FOR RESIDUE GOL D 157
22CC4SOFTWAREGLU D:39 , ALA D:42 , GLN D:43 , VAL D:47 , ALA D:48 , LEU D:49 , HOH D:550BINDING SITE FOR RESIDUE GOL D 158

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LWZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LWZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LWZ)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_YERPE10-27
 
 
 		  4A:10-27
B:10-27
C:10-27
D:10-27
Biological Unit 1 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_YERPE10-27
 
 
 		  12A:10-27
B:10-27
C:10-27
D:10-27

(-) Exons   (0, 0)

(no "Exon" information available for 3LWZ)

(-) 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:146
 aligned with AROQ_YERPE | Q8ZAX1 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           AROQ_YERPE     4 KFHILLLNGPNLNLLGTREPEKYGYTTLAEIVSQLEIQAQGMDVALSHLQSNAEHALIDSIHQARGNTDFILINPAAFTHTSVALRDALLGVQIPFIEIHLSNVHAREPFRHHSYLSDIAVGVICGLGADGYNFALQAAVNRLSKS 149
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------DEHYDROQUINASE_II -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwz A   4 KFHILLLNGPNLNLLGTREPEKYGYTTLAEIVSQLEIQAQGMDVALSHLQSNAEHALIDSIHQARGNTDFILINPAAFTHTSVALRDALLGVQIPFIEIHLSNVHAREPFRHHSYLSDIAVGVICGLGADGYNFALQAAVNRLSKS 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with AROQ_YERPE | Q8ZAX1 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     
           AROQ_YERPE     4 KFHILLLNGPNLNLLGTREPEKYGYTTLAEIVSQLEIQAQGMDVALSHLQSNAEHALIDSIHQARGNTDFILINPAAFTHTSVALRDALLGVQIPFIEIHLSNVHAREPFRHHSYLSDIAVGVICGLGADGYNFALQAAVNRLSK 148
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhh....eeeeehhhhhh.hhhhhhhhhhhh..eeeee.......hhhhhh..hhhhh.eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------DEHYDROQUINASE_II ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwz B   4 KFHILLLNGPNLNLLGTREPEKYGYTTLAEIVSQLEIQAQGMDVALSHLQSNAEHALIDSIHQARGNTDFILINPAAFTHTSVALRDALLGVQIPFIEIHLSNVHAREPFRHHSYLSDIAVGVICGLGADGYNFALQAAVNRLSK 148
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     


Chain C from PDB  Type:PROTEIN  Length:148
 aligned with AROQ_YERPE | Q8ZAX1 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           AROQ_YERPE     1 MSDKFHILLLNGPNLNLLGTREPEKYGYTTLAEIVSQLEIQAQGMDVALSHLQSNAEHALIDSIHQARGNTDFILINPAAFTHTSVALRDALLGVQIPFIEIHLSNVHAREPFRHHSYLSDIAVGVICGLGADGYNFALQAAVNRLSK 148
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh........eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------DEHYDROQUINASE_II ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwz C   1 MSDKFHILLLNGPNLNLLGTREPEKYGYTTLAEIVSQLEIQAQGMDVALSHLQSNAEHALIDSIHQARGNTDFILINPAAFTHTSVALRDALLGVQIPFIEIHLSNVHAREPFRHHSYLSDIAVGVICGLGADGYNFALQAAVNRLSK 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


Chain D from PDB  Type:PROTEIN  Length:147
 aligned with AROQ_YERPE | Q8ZAX1 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       
           AROQ_YERPE     3 DKFHILLLNGPNLNLLGTREPEKYGYTTLAEIVSQLEIQAQGMDVALSHLQSNAEHALIDSIHQARGNTDFILINPAAFTHTSVALRDALLGVQIPFIEIHLSNVHAREPFRHHSYLSDIAVGVICGLGADGYNFALQAAVNRLSKS 149
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --DHquinase_II-3lwzD01 D:5-144                                                                                                                ----- Pfam domains (1)
           Pfam domains (2) --DHquinase_II-3lwzD02 D:5-144                                                                                                                ----- Pfam domains (2)
           Pfam domains (3) --DHquinase_II-3lwzD03 D:5-144                                                                                                                ----- Pfam domains (3)
           Pfam domains (4) --DHquinase_II-3lwzD04 D:5-144                                                                                                                ----- Pfam domains (4)
         Sec.struct. author ...eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh........eeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------DEHYDROQUINASE_II -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwz D   3 DKFHILLLNGPNLNLLGTREPEKYGYTTLAEIVSQLEIQAQGMDVALSHLQSNAEHALIDSIHQARGNTDFILINPAAFTHTSVALRDALLGVQIPFIEIHLSNVHAREPFRHHSYLSDIAVGVICGLGADGYNFALQAAVNRLSKS 149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142
   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 3LWZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LWZ)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: DHquinase_II] (16)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (AROQ_YERPE | Q8ZAX1)
molecular function
    GO:0003855    3-dehydroquinate dehydratase activity    Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

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