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(-) Description

Title :  CRYSTAL STRUCTURE AT 1.8 ANGSTROM OF CDP-D-GLUCOSE 4,6-DEHYDRATASE FROM YERSINIA PSEUDOTUBERCULOSIS
 
Authors :  E. M. Vogan, C. Bellamacina, X. He, H. W. Liu, D. Ringe, G. A. Petsko
Date :  23 Nov 03  (Deposition) - 30 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dehydratase, Sdr, Cdp Glucose Dehydratase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Vogan, C. Bellamacina, X. He, H. W. Liu, D. Ringe, G. A. Petsko
Crystal Structure At 1. 8 A Resolution Of Cdp-D-Glucose 4, 6-Dehydratase From Yersinia Pseudotuberculosis
Biochemistry V. 43 3057 2004
PubMed-ID: 15023057  |  Reference-DOI: 10.1021/BI035547F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CDP-GLUCOSE-4,6-DEHYDRATASE
    Chains: A, B, C, D
    EC Number: 4.2.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJT8
    Expression System Strain: HB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ASCB
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
    Organism Taxid: 633

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:16 , THR A:18 , GLY A:19 , PHE A:20 , LYS A:21 , SER A:40 , LEU A:41 , GLY A:64 , ASP A:65 , ILE A:66 , ARG A:67 , MET A:87 , ALA A:88 , ALA A:89 , PRO A:91 , THR A:106 , ILE A:130 , THR A:131 , SER A:132 , TYR A:157 , LYS A:161 , ALA A:193 , GLY A:194 , ASN A:195 , VAL A:196 , HOH A:362 , HOH A:386 , HOH A:392 , HOH A:426 , HOH A:429 , HOH A:442 , HOH A:476 , HOH A:487 , HOH A:498 , HOH A:552BINDING SITE FOR RESIDUE NAD A 360
2AC2SOFTWAREGLY B:16 , THR B:18 , GLY B:19 , PHE B:20 , LYS B:21 , SER B:40 , LEU B:41 , GLY B:64 , ASP B:65 , ILE B:66 , ARG B:67 , MET B:87 , ALA B:88 , ALA B:89 , PRO B:91 , THR B:106 , ILE B:130 , THR B:131 , SER B:132 , TYR B:157 , LYS B:161 , ALA B:193 , GLY B:194 , ASN B:195 , VAL B:196 , ARG B:206 , HOH B:380 , HOH B:397 , HOH B:415 , HOH B:461 , HOH B:476 , HOH B:487 , HOH B:520 , HOH B:525 , HOH B:529 , HOH B:544BINDING SITE FOR RESIDUE NAD B 360
3AC3SOFTWAREGLY C:16 , THR C:18 , GLY C:19 , PHE C:20 , LYS C:21 , SER C:40 , LEU C:41 , GLY C:64 , ASP C:65 , ILE C:66 , ARG C:67 , MET C:87 , ALA C:88 , ALA C:89 , PRO C:91 , THR C:106 , ILE C:130 , THR C:131 , SER C:132 , TYR C:157 , LYS C:161 , ALA C:193 , GLY C:194 , ASN C:195 , VAL C:196 , HOH C:369 , HOH C:372 , HOH C:396 , HOH C:440 , HOH C:442 , HOH C:494 , HOH C:517BINDING SITE FOR RESIDUE NAD C 360
4AC4SOFTWAREGLY D:16 , THR D:18 , GLY D:19 , PHE D:20 , LYS D:21 , SER D:40 , LEU D:41 , GLY D:64 , ASP D:65 , ILE D:66 , ARG D:67 , MET D:87 , ALA D:88 , ALA D:89 , PRO D:91 , THR D:106 , ILE D:130 , THR D:131 , SER D:132 , TYR D:157 , LYS D:161 , ALA D:193 , GLY D:194 , ASN D:195 , VAL D:196 , ARG D:206 , HOH D:371 , HOH D:381BINDING SITE FOR RESIDUE NAD D 360

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RKX)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:46 -Pro A:47
2Val B:46 -Pro B:47
3Val C:46 -Pro C:47
4Val D:46 -Pro D:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RKX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RKX)

(-) Exons   (0, 0)

(no "Exon" information available for 1RKX)

(-) 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:349
 aligned with Q57329_YERPU | Q57329 from UniProtKB/TrEMBL  Length:357

    Alignment length:356
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
         Q57329_YERPU     2 INNSFWQGKRVFVTGHTGFKGGWLSLWLQTMGATVKGYSLTAPTVPSLFETARVADGMQSEIGDIRDQNKLLESIREFQPEIVFHMAAQPLVRLSYSEPVETYSTNVMGTVYLLEAIRHVGGVKAVVNITSDKCYDNKEWIWGYRENEAMGGYDPYSNSKGCAELVTSSYRNSFFNPANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAIRPWQHVLEPLSGYLLLAQKLYTDGAEYAEGWNFGPNDADATPVKNIVEQMVKYWGEGASWQLDGNAHPHEAHYLKLDCSKAKMQLGWHPRWNLNTTLEYIVGWHKNWLSGTDMHEYSITEINNYMNTK 357
               SCOP domains d1rkxa_ A: CDP-glucose-4,6-dehydratase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1rkxA01 A:2-193 NAD(P)-binding Rossmann-like Domain                                                                                                                                             1rkxA02 A:194-357 UDP-galactose 4-epimerase, domain 1                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhhh......eeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...ee........hhhhhhhhhhhh...ee......ee..eehhhhhhhhhhhhhhhhhhhhhhh.eee...hhhhheehhhhhhhhhhhhh....ee.-------........hhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rkx A   2 INNSFWQGKRVFVTGHTGFKGGWLSLWLQTMGATVKGYSLTAPTVPSLFETARVADGMQSEIGDIRDQNKLLESIREFQPEIVFHMAAQPLVRLSYSEPVETYSTNVMGTVYLLEAIRHVGGVKAVVNITSDKCYDNKEWIWGYRENEAMGGYDPYSNSKGCAELVTSSYRNSFFNPANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAIRPWQHVLEPLSGYLLLAQKLYTDGAEYAEGWNFGPNDADATPVKNIVEQMVKYWGEGASWQL-------EAHYLKLDCSKAKMQLGWHPRWNLNTTLEYIVGWHKNWLSGTDMHEYSITEINNYMNTK 357
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
                                                                                                                                                                                                                                                                                                                           291     299                                                          


Chain B from PDB  Type:PROTEIN  Length:346
 aligned with Q57329_YERPU | Q57329 from UniProtKB/TrEMBL  Length:357

    Alignment length:356
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
         Q57329_YERPU     2 INNSFWQGKRVFVTGHTGFKGGWLSLWLQTMGATVKGYSLTAPTVPSLFETARVADGMQSEIGDIRDQNKLLESIREFQPEIVFHMAAQPLVRLSYSEPVETYSTNVMGTVYLLEAIRHVGGVKAVVNITSDKCYDNKEWIWGYRENEAMGGYDPYSNSKGCAELVTSSYRNSFFNPANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAIRPWQHVLEPLSGYLLLAQKLYTDGAEYAEGWNFGPNDADATPVKNIVEQMVKYWGEGASWQLDGNAHPHEAHYLKLDCSKAKMQLGWHPRWNLNTTLEYIVGWHKNWLSGTDMHEYSITEINNYMNTK 357
               SCOP domains d1rkxb_ B: CDP-glucose-4,6-dehydratase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1rkxB01 B:2-193 NAD(P)-binding Rossmann-like Domain                                                                                                                                             1rkxB02 B:194-357 UDP-galactose 4-epimerase, domain 1                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhhh.hhhhheeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...ee........hhhhhhhhhhhh...ee......ee..eehhhhhhhhhhhhhhhhhhhhhhh.eee...hhhhheehhhhhhhhhhhhh....ee----------......hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rkx B   2 INNSFWQGKRVFVTGHTGFKGGWLSLWLQTMGATVKGYSLTAPTVPSLFETARVADGMQSEIGDIRDQNKLLESIREFQPEIVFHMAAQPLVRLSYSEPVETYSTNVMGTVYLLEAIRHVGGVKAVVNITSDKCYDNKEWIWGYRENEAMGGYDPYSNSKGCAELVTSSYRNSFFNPANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAIRPWQHVLEPLSGYLLLAQKLYTDGAEYAEGWNFGPNDADATPVKNIVEQMVKYWGEGASWQ----------HYLKLDCSKAKMQLGWHPRWNLNTTLEYIVGWHKNWLSGTDMHEYSITEINNYMNTK 357
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        |-       301       311       321       331       341       351      
                                                                                                                                                                                                                                                                                                                          290        301                                                        


Chain C from PDB  Type:PROTEIN  Length:351
 aligned with Q57329_YERPU | Q57329 from UniProtKB/TrEMBL  Length:357

    Alignment length:356
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
         Q57329_YERPU     2 INNSFWQGKRVFVTGHTGFKGGWLSLWLQTMGATVKGYSLTAPTVPSLFETARVADGMQSEIGDIRDQNKLLESIREFQPEIVFHMAAQPLVRLSYSEPVETYSTNVMGTVYLLEAIRHVGGVKAVVNITSDKCYDNKEWIWGYRENEAMGGYDPYSNSKGCAELVTSSYRNSFFNPANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAIRPWQHVLEPLSGYLLLAQKLYTDGAEYAEGWNFGPNDADATPVKNIVEQMVKYWGEGASWQLDGNAHPHEAHYLKLDCSKAKMQLGWHPRWNLNTTLEYIVGWHKNWLSGTDMHEYSITEINNYMNTK 357
               SCOP domains d1rkxc_ C: CDP-glucose-4,6-dehydratase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1rkxC01 C:2-193 NAD(P)-binding Rossmann-like Domain                                                                                                                                             1rkxC02 C:194-357 UDP-galactose 4-epimerase, domain 1                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhhh.hhhhheeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...ee........hhhhhhhhhhhh...ee......ee..eehhhhhhhhhhhhhhhhhhhhhhh.eee...hhhhheehhhhhhhhhhhhh....ee.-----..........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rkx C   2 INNSFWQGKRVFVTGHTGFKGGWLSLWLQTMGATVKGYSLTAPTVPSLFETARVADGMQSEIGDIRDQNKLLESIREFQPEIVFHMAAQPLVRLSYSEPVETYSTNVMGTVYLLEAIRHVGGVKAVVNITSDKCYDNKEWIWGYRENEAMGGYDPYSNSKGCAELVTSSYRNSFFNPANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAIRPWQHVLEPLSGYLLLAQKLYTDGAEYAEGWNFGPNDADATPVKNIVEQMVKYWGEGASWQL-----PHEAHYLKLDCSKAKMQLGWHPRWNLNTTLEYIVGWHKNWLSGTDMHEYSITEINNYMNTK 357
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     | 301       311       321       331       341       351      
                                                                                                                                                                                                                                                                                                                           291   297                                                            


Chain D from PDB  Type:PROTEIN  Length:347
 aligned with Q57329_YERPU | Q57329 from UniProtKB/TrEMBL  Length:357

    Alignment length:356
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
         Q57329_YERPU     2 INNSFWQGKRVFVTGHTGFKGGWLSLWLQTMGATVKGYSLTAPTVPSLFETARVADGMQSEIGDIRDQNKLLESIREFQPEIVFHMAAQPLVRLSYSEPVETYSTNVMGTVYLLEAIRHVGGVKAVVNITSDKCYDNKEWIWGYRENEAMGGYDPYSNSKGCAELVTSSYRNSFFNPANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAIRPWQHVLEPLSGYLLLAQKLYTDGAEYAEGWNFGPNDADATPVKNIVEQMVKYWGEGASWQLDGNAHPHEAHYLKLDCSKAKMQLGWHPRWNLNTTLEYIVGWHKNWLSGTDMHEYSITEINNYMNTK 357
               SCOP domains d1rkxd_ D: CDP-glucose-4,6-dehydratase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1rkxD01 D:2-193 NAD(P)-binding Rossmann-like Domain                                                                                                                                             1rkxD02 D:194-357 UDP-galactose 4-epimerase, domain 1                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhhh.hhhhheeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...ee........hhhhhhhhhhhh...ee......ee..eehhhhhhhhhhhhhhhhhhhhhhh.eee...hhhhheehhhhhhhhhhhhh....ee.---------......hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rkx D   2 INNSFWQGKRVFVTGHTGFKGGWLSLWLQTMGATVKGYSLTAPTVPSLFETARVADGMQSEIGDIRDQNKLLESIREFQPEIVFHMAAQPLVRLSYSEPVETYSTNVMGTVYLLEAIRHVGGVKAVVNITSDKCYDNKEWIWGYRENEAMGGYDPYSNSKGCAELVTSSYRNSFFNPANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAIRPWQHVLEPLSGYLLLAQKLYTDGAEYAEGWNFGPNDADATPVKNIVEQMVKYWGEGASWQL---------HYLKLDCSKAKMQLGWHPRWNLNTTLEYIVGWHKNWLSGTDMHEYSITEINNYMNTK 357
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
                                                                                                                                                                                                                                                                                                                           291       301
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RKX)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q57329_YERPU | Q57329)
molecular function
    GO:0047733    CDP-glucose 4,6-dehydratase activity    Catalysis of the reaction: CDP-D-glucose = CDP-4-dehydro-6-deoxy-D-glucose + 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.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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  1rkx
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  Q57329_YERPU | Q57329
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