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(-) Description

Title :  CRYSTAL STRUCTURE OF YAGE, A KDG ALDOLASE PROTEIN IN COMPLEX WITH 2-KETO-3-DEOXY GLUCONATE
 
Authors :  P. Manoj Kumar, V. Bhaskar, S. Manicka, S. Krishnaswamy
Date :  29 Jan 14  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Nal Superfamily, Aldolase Class I, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Manoj Kumar, V. Bhaskar, S. Manicka, S. Krishnaswamy
Crystal Structure Of Yage, A Kdg Aldolase Protein In Comple With 2-Keto-3-Deoxy Gluconate
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE 2-KETO-3-DEOXY-GALACTONATE ALDOLASE YAGE
    Chains: A, B, C, D
    EC Number: 4.1.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B0268, JW0261, YAGE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: PROBABLE KDGAL ALDOLASE YAGE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 32)

Asymmetric/Biological Unit (3, 32)
No.NameCountTypeFull Name
1EDO15Ligand/Ion1,2-ETHANEDIOL
2GOL13Ligand/IonGLYCEROL
3KDG4Ligand/Ion2-KETO-3-DEOXYGLUCONATE

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:54 , PHE A:60 , GLY A:88 , THR A:89 , GLY A:90 , VAL A:113 , VAL A:114 , ILE A:115BINDING SITE FOR RESIDUE EDO A 401
02AC2SOFTWARETHR A:139 , PRO A:141 , SER A:168 , ASN A:169BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREGLU A:271 , LEU A:275 , LYS A:296 , ARG D:73BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWARESER A:123 , GLU A:124BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWARETHR A:263 , SER B:123 , EDO B:403BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWAREPRO A:20 , PHE A:52 , GLY A:55 , SER A:56 , GLY A:57 , TYR A:145 , LYS A:174 , THR A:176 , GLY A:202 , TYR A:203 , ILE A:219 , SER A:220 , ALA A:221 , HOH A:532BINDING SITE FOR RESIDUE KDG A 406
07AC7SOFTWAREPHE B:25 , GLY B:29 , LEU B:31 , GLU B:67BINDING SITE FOR RESIDUE EDO B 401
08AC8SOFTWARELEU 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 402
09AC9SOFTWAREGOL A:405 , GLU B:124 , ALA B:125BINDING SITE FOR RESIDUE EDO B 403
10BC1SOFTWAREASP B:178 , SER B:179 , ASP D:178 , SER D:179BINDING SITE FOR RESIDUE EDO B 404
11BC2SOFTWAREGLY B:64 , ALA B:65 , GLU B:66 , GLU B:67BINDING SITE FOR RESIDUE GOL B 405
12BC3SOFTWARETHR B:15 , GLY B:16 , LEU B:211 , ASP B:216 , LEU B:234 , ARG B:238BINDING SITE FOR RESIDUE GOL B 406
13BC4SOFTWAREGLU B:66 , LYS B:69 , ALA B:70 , ARG B:73 , HIS B:103BINDING SITE FOR RESIDUE GOL B 407
14BC5SOFTWAREGLN B:153 , ASP B:154 , HOH B:649BINDING SITE FOR RESIDUE GOL B 408
15BC6SOFTWAREPRO B:20 , PHE B:52 , GLY B:55 , SER B:56 , GLY B:57 , TYR B:145 , LYS B:174 , THR B:176 , GLY B:202 , SER B:220 , ALA B:221 , HOH B:642BINDING SITE FOR RESIDUE KDG B 409
16BC7SOFTWARELEU C:54 , PHE C:60 , GLY C:88 , THR C:89 , GLY C:90 , VAL C:113 , ILE C:115 , TYR C:145BINDING SITE FOR RESIDUE EDO C 401
17BC8SOFTWARESER C:123 , GLU C:124 , ALA C:125 , EDO C:405BINDING SITE FOR RESIDUE EDO C 402
18BC9SOFTWAREGLU C:124 , ALA C:158 , LEU C:159 , THR C:162BINDING SITE FOR RESIDUE EDO C 403
19CC1SOFTWARESER C:179BINDING SITE FOR RESIDUE EDO C 404
20CC2SOFTWARESER C:123 , EDO C:402BINDING SITE FOR RESIDUE EDO C 405
21CC3SOFTWAREALA C:164 , ASP C:165 , SER C:166 , ARG C:167 , SER C:168BINDING SITE FOR RESIDUE GOL C 406
22CC4SOFTWARELEU B:31 , LYS B:33 , PRO B:34 , ASP C:32BINDING SITE FOR RESIDUE EDO C 407
23CC5SOFTWAREPRO C:20 , PHE C:52 , GLY C:55 , SER C:56 , GLY C:57 , TYR C:145 , LYS C:174 , THR C:176 , GLY C:202 , ILE C:219 , SER C:220 , ALA C:221 , HOH C:533BINDING SITE FOR RESIDUE KDG C 408
24CC6SOFTWAREGLU D:66 , LYS D:69BINDING SITE FOR RESIDUE EDO D 401
25CC7SOFTWAREGLN C:62 , PRO C:287 , THR D:92 , PRO D:117 , TYR D:118 , TYR D:119 , TRP D:120BINDING SITE FOR RESIDUE EDO D 402
26CC8SOFTWARELEU D:54 , PHE D:60 , GLY D:88 , THR D:89 , GLY D:90 , VAL D:113 , VAL D:114 , ILE D:115BINDING SITE FOR RESIDUE EDO D 403
27CC9SOFTWAREASP D:42 , ARG D:278 , HOH D:543BINDING SITE FOR RESIDUE GOL D 404
28DC1SOFTWARESER D:123 , GLU D:124 , ALA D:125BINDING SITE FOR RESIDUE EDO D 405
29DC2SOFTWARELYS A:33 , ALA D:164 , ASP D:165 , ARG D:167 , SER D:168BINDING SITE FOR RESIDUE GOL D 406
30DC3SOFTWARETHR D:15 , ASP D:216 , ARG D:238BINDING SITE FOR RESIDUE GOL D 407
31DC4SOFTWAREGLU A:293 , LYS D:69 , ARG D:73 , HIS D:103BINDING SITE FOR RESIDUE GOL D 408
32DC5SOFTWAREPRO D:20 , PHE D:52 , GLY D:55 , SER D:56 , GLY D:57 , TYR D:145 , LYS D:174 , THR D:176 , GLY D:202 , TYR D:203 , ALA D:221 , HOH D:518BINDING SITE FOR RESIDUE KDG D 409

(-) SS Bonds  (0, 0)

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

(-) 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 4ONV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ONV)

(-) 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..............hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4onv 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..............hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4onv 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..............hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4onv 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..............hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4onv 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 4ONV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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 Related Entries

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

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        YAGE_ECOLI | P75682: 2v8z 2v9d 3n2x 3nev 4oe7 4ptn 4u4m

(-) Related Entries Specified in the PDB File

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