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(-) Description

Title :  CRYSTAL STRUCTURE OF YAGE, A KDG ALDOLASE PROTEIN, IN COMPLEX WITH ALDOL CONDENSED PRODUCT OF PYRUVATE AND GLYOXAL
 
Authors :  P. Manoj Kumar, V. Baskar, S. Manicka, S. Krishnaswamy
Date :  12 Jan 14  (Deposition) - 24 Dec 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Aldolase Type I, Sugar Binding, Metal Coordination, Schiff Base, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Manoj Kumar, V. Baskar, S. Manicka, S. Krishnaswamy
Crystal Structure Of Yage, A Kdg Aldolase Protein, In Complex With Aldol Condensed Product Of Pyruvate And Glyoxa
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: K12
    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  (7, 43)

Asymmetric/Biological Unit (7, 43)
No.NameCountTypeFull Name
1EDO27Ligand/Ion1,2-ETHANEDIOL
2GOL5Ligand/IonGLYCEROL
3GXP2Ligand/Ion(4S)-4-HYDROXY-2,5-DIOXOPENTANOIC ACID
4GXS2Ligand/Ion(4R)-4-HYDROXY-2,5-DIOXOPENTANOIC ACID
5GXT1Ligand/IonETHANEDIAL
6MG4Ligand/IonMAGNESIUM ION
7PYR2Ligand/IonPYRUVIC ACID

(-) Sites  (43, 43)

Asymmetric Unit (43, 43)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:54 , PHE A:60 , ARG A:68 , GLY A:88 , THR A:89 , GLY A:90 , VAL A:113 , VAL A:114 , ILE A:115BINDING SITE FOR RESIDUE EDO A 401
02AC2SOFTWARELYS A:69 , ALA A:70 , ARG A:73 , HIS A:103 , HOH A:522 , ASP D:136BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREASP A:49 , VAL A:231 , LEU A:234 , LYS A:235 , ARG A:238BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWAREGLY A:57 , GXT A:409 , PYR A:410BINDING SITE FOR RESIDUE MG A 404
05AC5SOFTWARELEU A:54 , ARG A:68 , LYS A:69 , ALA A:72 , ILE A:87 , LEU A:100 , HIS A:103 , ALA A:104 , HOH A:507BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWARETHR A:92 , PRO A:117 , TYR A:118 , TYR A:119 , TRP A:120 , GLN B:62 , PRO B:287BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWAREASP A:178 , TYR A:203 , ASP A:205 , HIS A:206 , ALA C:181 , ARG C:184BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWARETHR A:156 , PRO A:157 , ALA A:158BINDING SITE FOR RESIDUE EDO A 408
09AC9SOFTWARESER A:56 , PHE A:147 , TYR A:203 , MG A:404 , PYR A:410 , HOH A:529BINDING SITE FOR RESIDUE GXT A 409
10BC1SOFTWAREPRO A:20 , PHE A:52 , GLY A:55 , SER A:56 , GLY A:57 , TYR A:145 , LYS A:174 , GLY A:202 , ILE A:219 , MG A:404 , GXT A:409 , HOH A:529BINDING SITE FOR RESIDUE PYR A 410
11BC2SOFTWARELEU B:54 , PHE B:60 , ARG B:68 , GLY B:88 , THR B:89 , GLY B:90 , VAL B:113 , VAL B:114 , ILE B:115BINDING SITE FOR RESIDUE EDO B 401
12BC3SOFTWAREGLY B:29 , GLN B:30 , LEU B:31 , GLU B:67 , ALA C:27BINDING SITE FOR RESIDUE GOL B 402
13BC4SOFTWAREALA B:181 , HIS B:182 , SER B:185 , GLN D:260BINDING SITE FOR RESIDUE GOL B 403
14BC5SOFTWARELYS B:244 , GLY B:247 , TYR B:248BINDING SITE FOR RESIDUE EDO B 404
15BC6SOFTWAREPRO B:20 , GLY B:57 , GXP B:410 , GXS B:411 , HOH B:512BINDING SITE FOR RESIDUE MG B 405
16BC7SOFTWAREPHE B:147 , ALA B:149 , ILE B:177 , ASP B:178 , TYR B:203 , HOH B:520BINDING SITE FOR RESIDUE EDO B 406
17BC8SOFTWAREGLY B:64 , ALA B:65 , GLU B:66 , GLU B:67BINDING SITE FOR RESIDUE EDO B 407
18BC9SOFTWAREARG A:95 , GLY B:29 , HIS B:283 , LEU B:285 , PRO B:286BINDING SITE FOR RESIDUE EDO B 408
19CC1SOFTWAREGLN A:62 , PRO A:287 , THR B:92 , PRO B:117 , TYR B:118 , TYR B:119 , TRP B:120BINDING SITE FOR RESIDUE EDO B 409
20CC2SOFTWAREPRO B:20 , PHE B:52 , GLY B:55 , SER B:56 , GLY B:57 , TYR B:145 , PHE B:147 , LYS B:174 , THR B:176 , GLY B:202 , MG B:405BINDING SITE FOR RESIDUE GXP B 410
21CC3SOFTWAREPRO B:20 , PHE B:52 , GLY B:55 , SER B:56 , GLY B:57 , TYR B:145 , PHE B:147 , LYS B:174 , THR B:176 , GLY B:202 , MG B:405 , HOH B:523BINDING SITE FOR RESIDUE GXS B 411
22CC4SOFTWARELEU C:54 , PHE C:60 , ARG C:68 , GLY C:88 , THR C:89 , GLY C:90 , VAL C:113 , VAL C:114 , ILE C:115 , TYR C:145BINDING SITE FOR RESIDUE EDO C 401
23CC5SOFTWAREASP C:49 , VAL C:231 , LEU C:234 , LYS C:235 , ARG C:238 , HOH C:540BINDING SITE FOR RESIDUE GOL C 402
24CC6SOFTWAREGLY C:57 , PYR C:412BINDING SITE FOR RESIDUE MG C 403
25CC7SOFTWARELEU C:54 , ARG C:68 , LYS C:69 , ALA C:72 , ILE C:87 , LEU C:100 , HIS C:103 , ALA C:104 , HOH C:517BINDING SITE FOR RESIDUE EDO C 404
26CC8SOFTWARETHR C:156 , PRO C:157 , ALA C:158BINDING SITE FOR RESIDUE EDO C 405
27CC9SOFTWAREALA A:181 , ARG A:184 , ASP C:178 , TYR C:203 , ASP C:205 , HIS C:206BINDING SITE FOR RESIDUE EDO C 406
28DC1SOFTWAREILE C:24 , ASP C:32 , GLY C:35 , PRO C:279 , VAL C:280 , SER C:281BINDING SITE FOR RESIDUE EDO C 407
29DC2SOFTWAREILE C:177 , ASP C:178 , TYR C:203BINDING SITE FOR RESIDUE EDO C 408
30DC3SOFTWAREGLN A:260 , ALA C:181 , ARG C:184BINDING SITE FOR RESIDUE EDO C 409
31DC4SOFTWAREGLY C:152 , GLN C:153 , ASP C:154BINDING SITE FOR RESIDUE EDO C 410
32DC5SOFTWAREPRO C:286 , PRO C:287 , ASN D:126 , ARG D:129 , TYR D:130 , GLN D:133BINDING SITE FOR RESIDUE EDO C 411
33DC6SOFTWAREPRO C:20 , PHE C:52 , GLY C:55 , SER C:56 , GLY C:57 , TYR C:145 , LYS C:174 , GLY C:202 , ILE C:219 , MG C:403 , HOH C:527BINDING SITE FOR RESIDUE PYR C 412
34DC7SOFTWARELYS C:121 , LEU C:150 , THR C:151 , GLY C:152 , HOH C:541 , HOH C:544 , LYS D:121 , PRO D:148 , ALA D:149 , GLY D:152BINDING SITE FOR RESIDUE EDO C 413
35DC8SOFTWAREALA B:181 , ARG B:184 , ASP D:178 , TYR D:203 , ASP D:205 , HIS D:206 , PRO D:256BINDING SITE FOR RESIDUE EDO D 401
36DC9SOFTWARELEU D:54 , PHE D:60 , ARG D:68 , GLY D:88 , THR D:89 , GLY D:90 , VAL D:113 , VAL D:114 , ILE D:115BINDING SITE FOR RESIDUE EDO D 402
37EC1SOFTWARETHR D:156 , PRO D:157 , ALA D:158BINDING SITE FOR RESIDUE EDO D 403
38EC2SOFTWAREASP D:42 , ASN D:224 , PRO D:227 , ARG D:278BINDING SITE FOR RESIDUE EDO D 404
39EC3SOFTWAREGLN D:153 , ASP D:154BINDING SITE FOR RESIDUE GOL D 405
40EC4SOFTWAREPRO D:20 , GLY D:57 , GXP D:408 , GXS D:409 , HOH D:524BINDING SITE FOR RESIDUE MG D 406
41EC5SOFTWAREPHE D:147 , ALA D:149 , ILE D:177 , ASP D:178 , TYR D:203 , HOH D:525BINDING SITE FOR RESIDUE EDO D 407
42EC6SOFTWAREPRO D:20 , PHE D:52 , GLY D:55 , SER D:56 , GLY D:57 , TYR D:145 , PHE D:147 , LYS D:174 , THR D:176 , GLY D:202 , ILE D:219 , MG D:406 , HOH D:537BINDING SITE FOR RESIDUE GXP D 408
43EC7SOFTWAREPRO D:20 , PHE D:52 , GLY D:55 , SER D:56 , GLY D:57 , TYR D:145 , PHE D:147 , LYS D:174 , THR D:176 , GLY D:202 , MG D:406 , HOH D:537BINDING SITE FOR RESIDUE GXS D 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OE7)

(-) 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 4OE7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OE7)

(-) Exons   (0, 0)

(no "Exon" information available for 4OE7)

(-) 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.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oe7 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....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oe7 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.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oe7 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..ee..........hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..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
                 4oe7 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)
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  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 4OE7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OE7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OE7)

(-) Gene Ontology  (6, 6)

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    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        YAGE_ECOLI | P75682: 2v8z 2v9d 3n2x 3nev 4onv 4ptn 4u4m

(-) Related Entries Specified in the PDB File

2v8z STRUCTURE OF NATIVE YAGE
3n2x STRUCTURE OF YAGE IN COMPLEX WITH PYRUVATE
3nev STRUCTURE OF YAGE IN COMPLEX WITH 2-KETO-3-DEOXY GALACTONATE