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(-) Description

Title :  CRYSTAL STRUCTURE OF 0.5M UREA UNFOLDED YAGE, A KDG ALDOLASE PROTEIN IN COMPLEX WITH PYRUVATE
 
Authors :  P. Manoj Kumar, V. Bhaskar, S. Manicka, S. Krishnaswamy
Date :  24 Jul 14  (Deposition) - 29 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Nal Superfamily, Kdga, Schiff Base, Catalytic Triad, Chemical Denaturant, Urea Promoted Unfolding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Manoj Kumar, V. Bhaskar, S. Manicka, S. Krishnaswamy
Crystal Structure Of 0. 5M Urea Unfolded Yage, A Kdg Aldolas Protein In Complex With Pyruvate
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YAGE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YAGE
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2PYR4Ligand/IonPYRUVIC ACID
3URE10Ligand/IonUREA

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:147 , THR A:176 , PHE A:265 , PYR A:404binding site for residue URE A 401
02AC2SOFTWAREASP A:178 , TYR A:203 , ASP A:205 , PRO A:256 , ALA C:181 , ARG C:184binding site for residue URE A 402
03AC3SOFTWAREASN A:93 , ARG A:95 , GLU A:96 , GLU A:99 , GLU B:67binding site for residue URE A 403
04AC4SOFTWAREPRO A:20 , PHE A:52 , GLY A:55 , SER A:56 , GLY A:57 , TYR A:145 , LYS A:174 , ILE A:219 , URE A:401binding site for residue PYR A 404
05AC5SOFTWARELEU A:54 , PHE A:60 , GLY A:90 , VAL A:113 , ILE A:115 , TYR A:145binding site for residue EDO A 407
06AC6SOFTWAREALA A:107binding site for residue EDO A 408
07AC7SOFTWAREGLY B:202 , TYR B:203 , ALA B:221 , PHE B:265 , PYR B:405binding site for residue URE B 401
08AC8SOFTWAREARG B:73 , ASP B:77 , GLU C:293binding site for residue URE B 402
09AC9SOFTWARELEU B:31 , GLU B:67binding site for residue URE B 403
10AD1SOFTWAREARG A:129 , ASP B:262 , SER B:289 , PRO B:290binding site for residue URE B 404
11AD2SOFTWARELEU B:54 , PHE B:60 , GLY B:88 , GLY B:90 , VAL B:113 , VAL B:114 , ILE B:115binding site for residue EDO B 406
12AD3SOFTWAREHIS B:283binding site for residue EDO B 407
13AD4SOFTWARELYS B:191 , PRO B:195binding site for residue EDO B 408
14AD5SOFTWAREASP B:77 , GLU C:271 , LYS C:296binding site for residue URE C 401
15AD6SOFTWAREPHE D:147 , THR D:176 , GLY D:202 , PHE D:265 , PYR D:403 , HOH D:501binding site for residue URE D 401
16AD7SOFTWAREARG C:129 , ASP D:262 , SER D:289 , PRO D:290binding site for residue URE D 402
17AD8SOFTWARELYS D:161 , ASP D:165binding site for residue EDO D 404
18AD9SOFTWAREALA D:12binding site for residue EDO D 405
19AE1SOFTWAREGLY D:47 , VAL D:48 , ASP D:49binding site for residue EDO D 406
20AE2SOFTWAREPRO B:20 , PHE B:52 , GLY B:55 , SER B:56 , GLY B:57 , LEU B:144 , TYR B:145 , ASN B:146 , ILE B:173 , ASP B:175 , THR B:176 , LEU B:200 , ILE B:219 , URE B:401binding site for Di-peptide PYR B 405 and LYS B 174
21AE3SOFTWAREPRO C:20 , PHE C:52 , GLY C:55 , SER C:56 , GLY C:57 , LEU C:144 , TYR C:145 , ASN C:146 , ILE C:173 , ASP C:175 , THR C:176 , LEU C:200 , ILE C:219binding site for Di-peptide PYR C 402 and LYS C 174
22AE4SOFTWAREPRO D:20 , PHE D:52 , GLY D:55 , SER D:56 , GLY D:57 , LEU D:144 , TYR D:145 , ASN D:146 , ILE D:173 , ASP D:175 , THR D:176 , LEU D:200 , ILE D:219 , URE D:401binding site for Di-peptide PYR D 403 and LYS D 174

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U4M)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Thr A:263 -Pro A:264
2Pro A:286 -Pro A:287
3Thr B:263 -Pro B:264
4Pro B:286 -Pro B:287
5Thr C:263 -Pro C:264
6Pro C:286 -Pro C:287
7Thr D:263 -Pro D:264
8Pro D:286 -Pro D:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U4M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U4M)

(-) Exons   (0, 0)

(no "Exon" information available for 4U4M)

(-) 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:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..............hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4m A  12 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 309
                                    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        


Chain B from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..ee..........hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4m B  12 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 309
                                    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        


Chain C from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..............hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4m C  12 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 309
                                    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        


Chain D from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..............hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4m D  12 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC 309
                                    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
   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 4U4M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U4M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U4M)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  4u4m
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  YAGE_ECOLI | P75682
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 Related Entries

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

UniProtKB/Swiss-Prot
        YAGE_ECOLI | P75682: 2v8z 2v9d 3n2x 3nev 4oe7 4onv 4ptn

(-) Related Entries Specified in the PDB File

2v8z NATIVE STRUCTURE OF PROTEIN YAGE
3n2x SAME PROTEIN IN COMPLEX WITH PYRUVATE