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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SOLUBLE ALDOSE SUGAR DEHYDROGENASE (ASD) FROM ESCHERICHIA COLI IN THE APO-FORM
 
Authors :  S. M. Southall, J. J. Doel, D. J. Richardson, A. Oubrie
Date :  03 Mar 06  (Deposition) - 08 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  6 Bladed Beta-Propellor, Pyrolloquinoline Quinone (Pqq), Quinoprotein, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Southall, J. J. Doel, D. J. Richardson, A. Oubrie
Soluble Aldose Sugar Dehydrogenase From Escherichia Coli: A Highly Exposed Active Site Conferring Broad Substrate Specificity.
J. Biol. Chem. V. 281 30650 2006
PubMed-ID: 16864586  |  Reference-DOI: 10.1074/JBC.M601783200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE/SORBOSONE DEHYDROGENASES
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET M-11
    Expression System Strain: B843 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YLII
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: K-12

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 40)

Asymmetric Unit (4, 40)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO25Ligand/Ion1,2-ETHANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO13Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 18)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU B:220 , TYR B:230 , HOH B:3023 , HOH B:3024 , HOH B:3038 , HOH B:3043BINDING SITE FOR RESIDUE CA B 2001
02AC2SOFTWAREGLU A:220 , TYR A:230 , HOH A:3027 , HOH A:3029 , HOH A:3037 , HOH A:3060BINDING SITE FOR RESIDUE CA A 2002
03AC3SOFTWARETHR A:114 , VAL A:115 , PHE A:116 , ARG A:117 , HOH A:3105 , HOH A:3502 , GLY B:44 , HOH B:3252BINDING SITE FOR RESIDUE PO4 A 2003
04AC4SOFTWARELYS B:13 , ASP B:15 , LEU B:33 , HOH B:3162 , HOH B:3213 , HOH B:3326BINDING SITE FOR RESIDUE EDO B 3001
05AC5SOFTWAREARG A:194 , GLU A:212 , GLY A:214 , GLY A:218 , TRP A:232 , THR A:236 , HOH A:3028 , HOH A:3037BINDING SITE FOR RESIDUE EDO A 3002
06AC6SOFTWAREARG B:194 , GLU B:212 , GLY B:214 , GLY B:218 , TRP B:232 , THR B:236 , HOH B:3026 , HOH B:3043BINDING SITE FOR RESIDUE EDO B 3003
07AC7SOFTWARETRP B:18 , ARG B:131 , GLN B:197 , SER B:271 , GLY B:272 , ARG B:323 , ASP B:324BINDING SITE FOR RESIDUE EDO B 3004
08AC8SOFTWARETHR B:114 , VAL B:115 , ARG B:117 , HOH B:3422 , HOH B:3521 , HOH B:3542BINDING SITE FOR RESIDUE EDO B 3005
09AC9SOFTWARETRP A:18 , ARG A:131 , SER A:271 , GLY A:272 , ARG A:323 , ASP A:324BINDING SITE FOR RESIDUE EDO A 3006
10BC1SOFTWARETRP A:204 , GLN A:286 , VAL A:303 , GLY A:305 , EDO A:3024 , HOH A:3034BINDING SITE FOR RESIDUE EDO A 3007
11BC2SOFTWARETRP B:204 , GLN B:286 , VAL B:303 , GLY B:305 , HOH B:3029BINDING SITE FOR RESIDUE EDO B 3008
12BC3SOFTWAREHIS B:16 , ARG B:34 , GLY B:63BINDING SITE FOR RESIDUE EDO B 3009
13BC4SOFTWAREASP A:111 , VAL B:5 , ASP B:317 , ARG B:318 , ARG B:350 , EDO B:3022 , HOH B:3123 , HOH B:3446BINDING SITE FOR RESIDUE EDO B 3010
14BC5SOFTWARELYS A:13 , ASP A:15 , LEU A:33 , HOH A:3178 , HOH A:3181 , HOH A:3280 , HOH A:3320 , HOH A:3343BINDING SITE FOR RESIDUE EDO A 3011
15BC6SOFTWAREVAL A:7 , ARG A:318BINDING SITE FOR RESIDUE EDO A 3012
16BC7SOFTWAREPRO B:24 , HIS B:27 , ARG B:78 , LEU B:106 , HOH B:3441 , HOH B:3448 , HOH B:3535BINDING SITE FOR RESIDUE EDO B 3013
17BC8SOFTWAREPHE B:22 , MSE B:29 , TYR B:334 , HOH B:3060 , HOH B:3259 , HOH B:3320 , HOH B:3439BINDING SITE FOR RESIDUE EDO B 3014
18BC9SOFTWAREALA B:71 , PRO B:72 , ASP B:73 , ASP B:168 , GLN B:169 , HOH B:3055 , HOH B:3373BINDING SITE FOR RESIDUE EDO B 3015
19CC1SOFTWAREPRO A:24 , HIS A:27 , PHE A:74 , ARG A:78 , LEU A:106 , HOH A:3457 , HOH A:3467 , HOH A:3496BINDING SITE FOR RESIDUE EDO A 3016
20CC2SOFTWAREALA A:71 , PRO A:72 , ASP A:73 , ASP A:168 , GLN A:169 , HOH A:3083 , HOH A:3438BINDING SITE FOR RESIDUE EDO A 3017
21CC3SOFTWAREARG B:216 , TRP B:237 , LYS B:265BINDING SITE FOR RESIDUE EDO B 3018
22CC4SOFTWARETYR A:334 , LYS A:346 , EDO A:3020 , HOH A:3127 , HOH A:3437 , ARG B:117BINDING SITE FOR RESIDUE EDO A 3019
23CC5SOFTWAREPHE A:22 , MSE A:29 , PRO A:329 , TYR A:334 , EDO A:3019 , HOH A:3059 , HOH A:3209BINDING SITE FOR RESIDUE EDO A 3020
24CC6SOFTWAREARG A:216 , TRP A:237 , LYS A:265BINDING SITE FOR RESIDUE EDO A 3021
25CC7SOFTWAREVAL B:7 , VAL B:9 , ARG B:318 , EDO B:3010 , HOH B:3372BINDING SITE FOR RESIDUE EDO B 3022
26CC8SOFTWAREASP A:311 , GLY A:312 , HOH A:3410 , HOH A:3427 , HOH A:3498BINDING SITE FOR RESIDUE EDO A 3023
27CC9SOFTWARETRP A:204 , GLN A:286 , EDO A:3007 , HOH A:3193BINDING SITE FOR RESIDUE EDO A 3024
28DC1SOFTWAREHIS A:16 , ARG A:34 , GLY A:35 , HOH A:3445BINDING SITE FOR RESIDUE EDO A 3025

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G8S)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Mse A:119 -Pro A:120
2Trp A:232 -Pro A:233
3Mse B:119 -Pro B:120
4Trp B:232 -Pro B:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G8S)

(-) Exons   (0, 0)

(no "Exon" information available for 2G8S)

(-) Sequences/Alignments

Asymmetric 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:348
 aligned with YLII_ECOLI | P75804 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:348
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362        
           YLII_ECOLI    23 ATVNVEVLQDKLDHPWALAFLPDNHGMLITLRGGELRHWQAGKGLSAPLSGVPDVWAHGQGGLLDVVLAPDFAQSRRIWLSYSEVGDDGKAGTAVGYGRLSDDLSKVTDFRTVFRQMPKLSTGNHFGGRLVFDGKGYLFIALGENNQRPTAQDLDKLQGKLVRLTDQGEIPDDNPFIKESGARAEIWSYGIRNPQGMAMNPWSNALWLNEHGPRGGDEINIPQKGKNYGWPLATWGINYSGFKIPEAKGEIVAGTEQPVFYWKDSPAVSGMAFYNSDKFPQWQQKLFIGALKDKDVIVMSVNGDKVTEDGRILTDRGQRIRDVRTGPDGYLYVLTDESSGELLKVSPR 370
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee..eeeeee......eeeee...eeeeee...ee.................eeeeee..hhhhhheeeeeeeee.....eeeeeeeeee......eeeeeeeee..............eee....eeeeee....hhhhhhh......eeeeee....................eeee...eeeeeeee....eeeeeee.....eeee.......................................eee.....eeeeeee....hhhhh.eeeeee....eeeeeeee..eeeeeeeehhhhh..eeeeee.....eeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2g8s A   3 ATVNVEVLQDKLDHPWALAFLPDNHGmLITLRGGELRHWQAGKGLSAPLSGVPDVWAHGQGGLLDVVLAPDFAQSRRIWLSYSEVGDDGKAGTAVGYGRLSDDLSKVTDFRTVFRQmPKLSTGNHFGGRLVFDGKGYLFIALGENNQRPTAQDLDKLQGKLVRLTDQGEIPDDNPFIKESGVRAEIWSYGIRNPQGmAmNPWSNALWLNEHGPRGGDEINIPQKGKNYGWPLATWGINYSGFKIPEAKGEIVAGTEQPVFYWKDSPAVSGmAFYNSDKFPQWQQKLFIGALKDKDVIVmSVNGDKVTEDGRILTDRGQRIRDVRTGPDGYLYVLTDESSGELLKVSPR 350
                                    12        22      | 32        42        52        62        72        82        92       102       112      |122       132       142       152       162       172       182       192      |202       212       222       232       242       252       262       272|      282       292       302       312       322       332       342        
                                                     29-MSE                                                                                   119-MSE                                                                         199-MSE                                                                   273-MSE                     301-MSE                                             
                                                                                                                                                                                                                                201-MSE                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:347
 aligned with YLII_ECOLI | P75804 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:347
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       
           YLII_ECOLI    24 TVNVEVLQDKLDHPWALAFLPDNHGMLITLRGGELRHWQAGKGLSAPLSGVPDVWAHGQGGLLDVVLAPDFAQSRRIWLSYSEVGDDGKAGTAVGYGRLSDDLSKVTDFRTVFRQMPKLSTGNHFGGRLVFDGKGYLFIALGENNQRPTAQDLDKLQGKLVRLTDQGEIPDDNPFIKESGARAEIWSYGIRNPQGMAMNPWSNALWLNEHGPRGGDEINIPQKGKNYGWPLATWGINYSGFKIPEAKGEIVAGTEQPVFYWKDSPAVSGMAFYNSDKFPQWQQKLFIGALKDKDVIVMSVNGDKVTEDGRILTDRGQRIRDVRTGPDGYLYVLTDESSGELLKVSPR 370
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeee......eeeee...eeeeee...ee.................eeeeee..hhhhhheeeeeeeee.....eeeeeeeeee......eeeeeeeee..............eee....eeeeee....hhhhhhh......eeeeee....................eeee...eeeeeeee....eeeeeee.....eeee.......................................eee.....eeeeeee....hhhhh.eeeeee....eeeeeeee..eeeeeeeehhhhh..eeeeee.....eeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g8s B   4 TVNVEVLQDKLDHPWALAFLPDNHGmLITLRGGELRHWQAGKGLSAPLSGVPDVWAHGQGGLLDVVLAPDFAQSRRIWLSYSEVGDDGKAGTAVGYGRLSDDLSKVTDFRTVFRQmPKLSTGNHFGGRLVFDGKGYLFIALGENNQRPTAQDLDKLQGKLVRLTDQGEIPDDNPFIKESGVRAEIWSYGIRNPQGmAmNPWSNALWLNEHGPRGGDEINIPQKGKNYGWPLATWGINYSGFKIPEAKGEIVAGTEQPVFYWKDSPAVSGmAFYNSDKFPQWQQKLFIGALKDKDVIVmSVNGDKVTEDGRILTDRGQRIRDVRTGPDGYLYVLTDESSGELLKVSPR 350
                                    13        23     |  33        43        53        63        73        83        93       103       113     | 123       133       143       153       163       173       183       193     | 203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       
                                                    29-MSE                                                                                   119-MSE                                                                         199-MSE                                                                   273-MSE                     301-MSE                                             
                                                                                                                                                                                                                               201-MSE
   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 2G8S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G8S)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YLII_ECOLI | P75804)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016901    oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
    GO:0070968    pyrroloquinoline quinone binding    Interacting selectively and non-covalently with pyrroloquinoline quinone, PQQ, the coenzyme or the prosthetic group of certain alcohol dehydrogenases and glucose dehydrogenases.
    GO:0048038    quinone binding    Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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  2g8s
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  YLII_ECOLI | P75804
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 Related Entries

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