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(-) Description

Title :  X-RAY STRUCTURE OF H243I MUTANT OF UDP-GALACTOSE 4-EPIMERASE FROM E.COLI:EVIDENCE FOR EXISTENCE OF OPEN AND CLOSED ACTIVE SITE DURING CATALYSIS.
 
Authors :  N. Singh, P. Tiwari, S. Phulera, A. Dixit, D. Choudhury
Date :  21 Sep 16  (Deposition) - 30 Nov 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Induced Fit Mechanism, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Singh, P. Tiwari, S. Phulera, A. Dixit, D. Choudhury
X-Ray Structure Of H243I Mutant Of Udp-Galactose 4-Epimeras From E. Coli:Evidence For Existence Of Open And Closed Activ Site During Catalysis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-GLUCOSE 4-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B+
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GALE, GALD, B0759, JW0742
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: GALACTOWALDENASE,UDP-GALACTOSE 4-EPIMERASE
    Variant: W3110

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NO31Ligand/IonNITRATE ION
4UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:179 , ASN A:198 , ASN A:199 , LEU A:200 , ALA A:216 , ILE A:217 , PHE A:218 , ARG A:231 , TYR A:233 , VAL A:269 , ARG A:292 , ASP A:295 , HOH A:554 , HOH A:577 , HOH A:598 , HOH A:658 , HOH A:674 , HOH A:682 , HOH A:757binding site for residue UDP A 401
2AC2SOFTWAREGLY A:7 , GLY A:10 , TYR A:11 , ILE A:12 , ASP A:31 , ASN A:32 , LEU A:33 , CYS A:34 , ASN A:35 , SER A:36 , GLY A:57 , ASP A:58 , ILE A:59 , PHE A:80 , ALA A:81 , GLY A:82 , LYS A:84 , ASN A:99 , SER A:122 , SER A:123 , TYR A:149 , LYS A:153 , TYR A:177 , PHE A:178 , PRO A:180 , HOH A:523 , HOH A:547 , HOH A:559 , HOH A:592 , HOH A:595 , HOH A:638 , HOH A:650binding site for residue NAD A 402
3AC3SOFTWAREARG A:331 , HIS A:332 , HOH A:513 , HOH A:542 , HOH A:720 , ASN B:267 , THR B:317 , LEU B:318 , ASP B:319binding site for residue GOL A 403
4AC4SOFTWAREASN B:179 , ASN B:198 , ASN B:199 , LEU B:200 , ALA B:216 , ILE B:217 , PHE B:218 , ARG B:231 , TYR B:233 , VAL B:269 , ARG B:292 , ASP B:295 , HOH B:548 , HOH B:551 , HOH B:599 , HOH B:640 , HOH B:656 , HOH B:665 , HOH B:702 , HOH B:713binding site for residue UDP B 401
5AC5SOFTWAREGLY B:7 , GLY B:10 , TYR B:11 , ILE B:12 , ASP B:31 , ASN B:32 , LEU B:33 , CYS B:34 , ASN B:35 , SER B:36 , GLY B:57 , ASP B:58 , ILE B:59 , PHE B:80 , ALA B:81 , GLY B:82 , LYS B:84 , ASN B:99 , SER B:122 , SER B:123 , TYR B:149 , LYS B:153 , TYR B:177 , PHE B:178 , PRO B:180 , HOH B:519 , HOH B:555 , HOH B:579 , HOH B:582 , HOH B:593 , HOH B:615 , HOH B:626 , HOH B:632binding site for residue NAD B 402
6AC6SOFTWAREARG B:38 , PRO B:223 , ARG B:291 , PRO B:297 , HOH B:561binding site for residue NO3 B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GY7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:134 -Pro A:135
2Ile B:134 -Pro B:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GY7)

(-) Exons   (0, 0)

(no "Exon" information available for 5GY7)

(-) 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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eee.................hhhhhhhhhhh.....eeee...........ee.eeehhhhhhhhhhhhhhhh...eeeeeee.....eehhhhhhhhhhhhh....eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gy7 A   1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRNEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGIVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
                                    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       260       270       280       290       300       310       320       330        


Chain B from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhh..................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eee.................hhhhhhhhhhh.....eeee...........ee.eeehhhhhhhhhhhhhhhh...eeeeeee.....eehhhhhhhhhhhhh....eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gy7 B   1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRNEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGIVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
                                    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       260       270       280       290       300       310       320       330
   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  (0, 0)

(no "SCOP Domain" information available for 5GY7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GY7)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ile A:134 - Pro A:135   [ RasMol ]  
    Ile B:134 - Pro B:135   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GALE_ECOLI | P09147: 1a9y 1a9z 1kvq 1kvr 1kvs 1kvt 1kvu 1lrj 1lrk 1lrl 1nah 1nai 1uda 1udb 1udc 1xel 2udp

(-) Related Entries Specified in the PDB File

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