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(-) Description

Title :  STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO FLAVIN MONONUCLEOTIDE
 
Authors :  T. D. Gruber, M. C. Dimond, L. L. Kiessling, K. T. Forest
Date :  05 Dec 09  (Deposition) - 15 Dec 10  (Release) - 15 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Flavoenzyme, Protein-Ligand Complex, Carbohydrate Biosynthesis, Fad, Flavoprotein, Lipopolysaccharide Biosynthesis, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. D. Gruber, M. C. Dimond, L. L. Kiessling, K. T. Forest
Structure Of Udp-Galactopyranose Mutase Bound To Flavin Mononucleotide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE UDP-GALACTOPYRANOSE MUTASE
    Chains: A, B
    EC Number: 5.4.99.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEM-TEASY
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GLF, RFBD
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Strain: 01 (ATCC 13882)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:9 , GLY A:10 , GLY A:12 , PHE A:13 , SER A:14 , ASP A:33 , GLN A:34 , ARG A:35 , GLY A:40 , ASN A:41 , SER A:42 , PRO A:59 , HIS A:60 , ILE A:61 , ARG A:217 , PHE A:219 , TYR A:232 , SER A:233 , GLY A:234 , PRO A:235 , LEU A:252 , TYR A:313 , TYR A:314 , GLY A:342 , ARG A:343 , TYR A:349 , LEU A:350 , ASP A:351 , MET A:352 , THR A:355 , HOH A:394 , HOH A:398 , HOH A:403 , HOH A:421 , HOH A:432 , HOH A:465 , HOH A:477 , HOH A:497BINDING SITE FOR RESIDUE FAD A 391
2AC2SOFTWAREGLN A:159 , TRP A:160 , ARG A:174 , TYR A:185 , ARG A:280 , TYR A:314 , TYR A:349 , HOH A:498BINDING SITE FOR RESIDUE FMN A 392
3AC3SOFTWAREVAL B:9 , GLY B:10 , GLY B:12 , PHE B:13 , SER B:14 , ASP B:33 , GLN B:34 , ARG B:35 , GLY B:40 , ASN B:41 , PRO B:59 , HIS B:60 , ILE B:61 , ARG B:217 , PHE B:219 , SER B:233 , GLY B:234 , PRO B:235 , TYR B:313 , TYR B:314 , GLY B:342 , ARG B:343 , TYR B:349 , LEU B:350 , ASP B:351 , MET B:352 , THR B:355 , HOH B:396 , HOH B:399 , HOH B:405 , HOH B:406 , HOH B:407 , HOH B:426 , HOH B:435 , HOH B:440 , HOH B:474 , HOH B:535BINDING SITE FOR RESIDUE FAD B 391
4AC4SOFTWAREGLN B:159 , TRP B:160 , TYR B:185 , HIS B:188 , FMN B:393 , FMN B:394 , HOH B:442 , HOH B:462 , HOH B:511BINDING SITE FOR RESIDUE FMN B 392
5AC5SOFTWARETYR B:155 , GLN B:159 , TRP B:160 , TYR B:185 , TYR B:314 , TYR B:349 , FMN B:392 , HOH B:417 , HOH B:511 , HOH B:546BINDING SITE FOR RESIDUE FMN B 393
6AC6SOFTWAREPRO B:98 , PHE B:151 , PHE B:152 , THR B:156 , ILE B:171 , ARG B:174 , PRO B:176 , ARG B:178 , ASN B:187 , FMN B:392 , HOH B:418 , HOH B:457 , HOH B:476BINDING SITE FOR RESIDUE FMN B 394

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:97 -Pro A:98
2Leu B:97 -Pro B:98

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KYB)

(-) Exons   (0, 0)

(no "Exon" information available for 3KYB)

(-) 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:383
 aligned with GLF1_KLEPN | Q48485 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:383
                                    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       361       371       381   
           GLF1_KLEPN     2 KSKKILIVGAGFSGAVIGRQLAEKGHQVHIIDQRDHIGGNSYDARDSETNVMVHVYGPHIFHTDNETVWNYVNKHAEMMPYVNRVKATVNGQVFSLPINLHTINQFFSKTCSPDEARALIAEKGDSTIADPQTFEEQALRFIGKELYEAFFKGYTIKQWGMQPSELPASILKRLPVRFNYDDNYFNHKFQGMPKCGYTQMIKSILNHENIKVDLQREFIVEERTHYDHVFYSGPLDAFYGYQYGRLGYRTLDFKKFTYQGDYQGCAVMNYCSVDVPYTRITEHKYFSPWEQHDGSVCYKEYSRACEENDIPYYPIRQMGEMALLEKYLSLAENETNITFVGRLGTYRYLDMDVTIAEALKTAEVYLNSLTENQPMPVFTVSVR 384
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhh...eeeeee.....hhhh.eee......eee......eee.hhhhhhhhhh...eee....eeeee..eeeee..hhhhhhhhhh...hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...............eeeee.hhhhhhhhhhhh...eeeee....hhhhhhhh.eeee..hhhhhh........eeeeeeeeeeee.......eeee........eeee.hhhh......eeeeeeeeeee........ee..hhhhhhhhhhhhhhhh....eeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kyb A   2 KSKKILIVGAGFSGAVIGRQLAEKGHQVHIIDQRDHIGGNSYDARDSETNVMVHVYGPHIFHTDNETVWNYINKHAEMMPYVNRVKATVNGQVFSLPINLHTINQFFSKTCSPDEARALIAEKGDSTIADPQTFEEQALRFIGKELYEAFFKGYTIKQWGMQPSELPASILKRLPVRFNYDDNYFNHKFQGMPKCGYTQMIKSILNHENIKVDLQREFIVDERTHYDHVFYSGPLDAFYGYQYGRLGYRTLDFKKFIYQGDYQGCAVMNYCSVDVPYTRITEHKYFSPWEQHDGSVCYKEYSRACEENDIPYYPIRQMGEMALLEKYLSLAENETNITFVGRLGTYRYLDMDVTIAEALKTAEVYLNSLTDNQPMPVFTVSVG 384
                                    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       361       371       381   


Chain B from PDB  Type:PROTEIN  Length:381
 aligned with GLF1_KLEPN | Q48485 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:381
                                    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       361       371       381 
           GLF1_KLEPN     2 KSKKILIVGAGFSGAVIGRQLAEKGHQVHIIDQRDHIGGNSYDARDSETNVMVHVYGPHIFHTDNETVWNYVNKHAEMMPYVNRVKATVNGQVFSLPINLHTINQFFSKTCSPDEARALIAEKGDSTIADPQTFEEQALRFIGKELYEAFFKGYTIKQWGMQPSELPASILKRLPVRFNYDDNYFNHKFQGMPKCGYTQMIKSILNHENIKVDLQREFIVEERTHYDHVFYSGPLDAFYGYQYGRLGYRTLDFKKFTYQGDYQGCAVMNYCSVDVPYTRITEHKYFSPWEQHDGSVCYKEYSRACEENDIPYYPIRQMGEMALLEKYLSLAENETNITFVGRLGTYRYLDMDVTIAEALKTAEVYLNSLTENQPMPVFTVS 382
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------NAD_binding_8-3kybB03 B:8-76                                         -------------------------------------------------------------------------GLF-3kybB01 B:150-349                                                                                                                                                                                   --------------------------------- Pfam domains (1)
           Pfam domains (2) ------NAD_binding_8-3kybB04 B:8-76                                         -------------------------------------------------------------------------GLF-3kybB02 B:150-349                                                                                                                                                                                   --------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeee..hhhhhhhhhhhhh...eeeee......hhhh.eee......eee......eee.hhhhhhhhhh...eee....eeeee..eeeee..hhhhhhhhhh...hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.................eeeee.hhhhhhhhhhh....eeee.....hhhhhhhh.eeee..hhhhhh........eeeeeeeeeeee.......eeee........eeee.hhhh......eeeeeeeeeee........ee..hhhhhhhhhhhhhhhh....eeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kyb B   2 KSKKILIVGAGFSGAVIGRQLAEKGHQVHIIDQRDHIGGNSYDARDSETNVMVHVYGPHIFHTDNETVWNYINKHAEMMPYVNRVKATVNGQVFSLPINLHTINQFFSKTCSPDEARALIAEKGDSTIADPQTFEEQALRFIGKELYEAFFKGYTIKQWGMQPSELPASILKRLPVRFNYDDNYFNHKFQGMPKCGYTQMIKSILNHENIKVDLQREFIVDERTHYDHVFYSGPLDAFYGYQYGRLGYRTLDFKKFIYQGDYQGCAVMNYCSVDVPYTRITEHKYFSPWEQHDGSVCYKEYSRACEENDIPYYPIRQMGEMALLEKYLSLAENETNITFVGRLGTYRYLDMDVTIAEALKTAEVYLNSLTDNQPMPVFTVS 382
                                    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       361       371       381
   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 3KYB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GLF1_KLEPN | Q48485)
molecular function
    GO:0008767    UDP-galactopyranose mutase activity    Catalysis of the reaction: UDP-D-galactopyranose = UDP-D-galacto-1,4-furanose.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLF1_KLEPN | Q48485: 1wam 2bi7 2bi8 3gf4 3inr 3int

(-) Related Entries Specified in the PDB File

1wam STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE FROM KLEBSIELLA PNEUMONIAE WITH FADH-
2bi7 UDP-GALACTOPYRANOSE MUTASE FROM KLEBSIELLA PNEUMONIAE OXIDISED FAD
2bi8 UDP-GALACTOPYRANOSE MUTASE FROM KLEBSIELLA PNEUMONIAE WITH REDUCED FAD
3gf4 STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO UDP-GLUCOSE
3inr STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO UDP- GALACTOSE (OXIDIZED)
3int STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO UDP- GALACTOSE (REDUCED)