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(-) Description

Title :  CRYSTAL STRUCTURE OF YAGE, A KDG ALDOLASE PROTEIN IN COMPLEX WITH MAGNESIUM CATION COORDINATED L-GLYCERALDEHYDE
 
Authors :  P. Manoj Kumar, V. Baskar, S. Manicka, S. Krishnaswamy
Date :  11 Mar 14  (Deposition) - 03 Dec 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Nal Superfamily, Aldolase Class I, Metal Coordination, Lyase, Stereospecificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Manicka, Y. Peleg, T. Unger, S. Albeck, O. Dym, H. M. Greenblatt, G. Bourenkov, V. Lamzin, S. Krishnaswamy, J. L. Sussman
Crystal Structure Of Yage, A Putative Dhdps-Like Protein From Escherichia Coli K12.
Proteins V. 71 2102 2008
PubMed-ID: 18361457  |  Reference-DOI: 10.1002/PROT.22023
(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  (5, 22)

Asymmetric/Biological Unit (5, 22)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3GXV4Ligand/IonL-GLYCERALDEHYDE
4MG4Ligand/IonMAGNESIUM ION
5PYR2Ligand/IonPYRUVIC ACID

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:52 , LEU A:54 , GLY A:55 , PHE A:60 , GLY A:88 , GLY A:90 , VAL A:113 , VAL A:114 , ILE A:115 , TYR A:145BINDING SITE FOR RESIDUE EDO A 401
02AC2SOFTWAREASP A:178 , TYR A:203 , ASP A:205 , HIS A:206 , ALA C:181 , ARG C:184BINDING SITE FOR RESIDUE EDO A 402
03AC3SOFTWARELYS A:174 , THR A:176 , GLY A:202 , TYR A:203 , ILE A:219 , SER A:220 , ALA A:221 , PHE A:265 , MG A:404 , HOH A:524 , HOH A:532BINDING SITE FOR RESIDUE GXV A 403
04AC4SOFTWAREPRO A:20 , GLY A:57 , GXV A:403 , HOH A:524 , HOH A:532BINDING SITE FOR RESIDUE MG A 404
05AC5SOFTWARELEU B:54 , PHE B:60 , GLY B:88 , GLY B:90 , VAL B:113 , VAL B:114 , ILE B:115 , TYR B:145BINDING SITE FOR RESIDUE EDO B 401
06AC6SOFTWAREASP B:178 , TYR B:203 , ASP B:205 , HIS B:206 , PRO B:256 , ARG D:184BINDING SITE FOR RESIDUE EDO B 402
07AC7SOFTWARETYR B:248 , THR B:251 , LEU B:306BINDING SITE FOR RESIDUE EDO B 403
08AC8SOFTWAREPHE B:147 , ALA B:149 , ASP B:178 , TYR B:203 , HOH B:511BINDING SITE FOR RESIDUE EDO B 404
09AC9SOFTWAREASP B:178 , ASP D:178BINDING SITE FOR RESIDUE GOL B 405
10BC1SOFTWAREPRO B:20 , LYS B:174 , THR B:176 , GLY B:202 , TYR B:203 , ILE B:219 , SER B:220 , ALA B:221 , PHE B:265 , MG B:407 , HOH B:508 , HOH B:634BINDING SITE FOR RESIDUE GXV B 406
11BC2SOFTWAREPRO B:20 , SER B:56 , GLY B:57 , GXV B:406 , HOH B:508BINDING SITE FOR RESIDUE MG B 407
12BC3SOFTWAREALA A:125 , ASP B:262 , SER B:289 , PRO B:290 , ASP B:292 , HOH B:539 , HOH B:600BINDING SITE FOR RESIDUE PYR B 408
13BC4SOFTWARELEU 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:115BINDING SITE FOR RESIDUE EDO C 401
14BC5SOFTWAREALA A:181 , ARG A:184 , ASP C:178 , TYR C:203 , ASP C:205 , HIS C:206BINDING SITE FOR RESIDUE EDO C 402
15BC6SOFTWAREGLY C:64 , ALA C:65 , GLU C:66 , GLU C:67 , HOH C:609 , HOH C:625BINDING SITE FOR RESIDUE EDO C 403
16BC7SOFTWARELYS C:174 , THR C:176 , GLY C:202 , TYR C:203 , ILE C:219 , SER C:220 , ALA C:221 , PHE C:265 , MG C:405 , HOH C:528 , HOH C:603BINDING SITE FOR RESIDUE GXV C 404
17BC8SOFTWAREPRO C:20 , GLY C:57 , GXV C:404 , HOH C:528BINDING SITE FOR RESIDUE MG C 405
18BC9SOFTWAREALA 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
19CC1SOFTWAREPHE D:52 , LEU 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:115 , TYR D:145BINDING SITE FOR RESIDUE EDO D 402
20CC2SOFTWARELYS D:174 , GLY D:202 , TYR D:203 , ILE D:219 , SER D:220 , ALA D:221 , PHE D:265 , MG D:404 , HOH D:528 , HOH D:643BINDING SITE FOR RESIDUE GXV D 403
21CC3SOFTWAREPRO D:20 , SER D:56 , GLY D:57 , GXV D:403 , HOH D:528BINDING SITE FOR RESIDUE MG D 404
22CC4SOFTWAREASP D:262 , SER D:289 , PRO D:290 , ASP D:292 , HOH D:533 , HOH D:586 , HOH D:609BINDING SITE FOR RESIDUE PYR D 405

(-) SS Bonds  (0, 0)

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

(-) 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 4PTN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PTN)

(-) 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....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
                 4ptn 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..............hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ptn 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....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
                 4ptn 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....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
                 4ptn 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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  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 4PTN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4u4m

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4PTN)