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(-) Description

Title :  CRYSTAL STRUCTURES OF MANNONATE DEHYDRATASE FROM ESCHERICHIA COLI STRAIN K12 COMPLEXED WITH D-MANNONATE
 
Authors :  X. Qiu, Y. Zhu, Y. Yuan, Y. Zhang, H. Liu, Y. Gao, M. Teng, L. Niu
Date :  23 Mar 12  (Deposition) - 27 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Tim Barrel, Dehydratase, D-Mannonate Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Qiu, Y. Tao, Y. Zhu, Y. Yuan, Y. Zhang, H. Liu, Y. Gao, M. Teng, L. Niu
Structural Insights Into Decreased Enzymatic Activity Induced By An Insert Sequence In Mannonate Dehydratase From Gram Negative Bacterium.
J. Struct. Biol. V. 180 327 2012
PubMed-ID: 22796868  |  Reference-DOI: 10.1016/J.JSB.2012.06.013

(-) Compounds

Molecule 1 - MANNONATE DEHYDRATASE
    Chains: A, B, C, D
    EC Number: 4.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UXUA, B4322, JW4285
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: D-MANNONATE HYDROLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2CS22Ligand/IonD-MANNONIC ACID
3MN4Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CS21Ligand/IonD-MANNONIC ACID
3MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CS21Ligand/IonD-MANNONIC ACID
3MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CS2-1Ligand/IonD-MANNONIC ACID
3MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CS2-1Ligand/IonD-MANNONIC ACID
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:6 , ARG A:349 , PRO A:350 , ASP A:351 , ARG A:373BINDING SITE FOR RESIDUE CL A 401
02AC2SOFTWAREARG A:6 , GLU A:63 , ASN A:103 , ASP A:109 , TRP A:110 , HIS A:233 , ASP A:236 , CYS A:271 , SER A:274 , HIS A:298 , ARG A:300 , ARG A:349 , ASP A:351 , HIS A:352 , TYR A:368 , MN A:403 , HOH A:566 , HOH A:586BINDING SITE FOR RESIDUE CS2 A 402
03AC3SOFTWAREHIS A:233 , CYS A:271 , HIS A:298 , ASP A:351 , CS2 A:402BINDING SITE FOR RESIDUE MN A 403
04AC4SOFTWAREARG B:6 , ARG B:349 , PRO B:350 , ASP B:351 , ARG B:373BINDING SITE FOR RESIDUE CL B 401
05AC5SOFTWAREARG B:6 , GLU B:63 , ASN B:103 , ASP B:109 , TRP B:110 , HIS B:233 , ASP B:236 , CYS B:271 , SER B:274 , HIS B:298 , ARG B:300 , ARG B:349 , ASP B:351 , HIS B:352 , TYR B:368 , MN B:403 , HOH B:518 , HOH B:719BINDING SITE FOR RESIDUE CS2 B 402
06AC6SOFTWAREHIS B:233 , CYS B:271 , HIS B:298 , ASP B:351 , CS2 B:402BINDING SITE FOR RESIDUE MN B 403
07AC7SOFTWAREARG C:6 , ARG C:349 , PRO C:350 , ASP C:351 , ARG C:373BINDING SITE FOR RESIDUE CL C 401
08AC8SOFTWAREHIS C:233 , CYS C:271 , HIS C:298 , ASP C:351BINDING SITE FOR RESIDUE MN C 402
09AC9SOFTWAREARG D:6 , ARG D:349 , PRO D:350 , ASP D:351 , ARG D:373BINDING SITE FOR RESIDUE CL D 401
10BC1SOFTWAREHIS D:233 , CYS D:271 , HIS D:298 , ASP D:351BINDING SITE FOR RESIDUE MN D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Glu A:63 -Ser A:64
2Pro A:144 -Gly A:145
3Asp A:236 -Pro A:237
4Glu B:63 -Ser B:64
5Arg B:194 -Lys B:195
6Asp B:236 -Pro B:237
7Glu C:63 -Ser C:64
8Asp C:236 -Pro C:237
9Glu D:63 -Ser D:64
10Asp D:236 -Pro D:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EAY)

(-) 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:395
                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee........hhhhhhhhh..eeee...........hhhhhhhhhhhhhh...eeeeee....hhhhhhh..hhhhhhhhhhhhhhhhhhh...eeee...........eeeee.....eeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.eeee.................hhhhhhhhhhhh....eeeeeehhhhh.....hhhhhhhhhh..eeeee...eee......eee........hhhhhhhhhhhhhhhhhhh.......ee......hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eay A  -1 SHMEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSVVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGLPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRSTMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFS 393
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388     


Chain B from PDB  Type:PROTEIN  Length:395
                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee........hhhhhhhhh..eeee...........hhhhhhhhhhhhhhh..eeeeee....hhhhhhh..hhhhhhhhhhhhhhhhhhh...eeee...........eeeee.....eeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.eeee.................hhhhhhhhhhhh....eeeeeehhhhh.....hhhhhhhhhh..eeeee...eee......eee........hhhhhhhhhhhhhhhhhhh.......ee......hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eay B  -1 SHMEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSVVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGLPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRSTMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFS 393
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388     


Chain C from PDB  Type:PROTEIN  Length:396
                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee........hhhhhhhh...eeee...........hhhhhhhhhhhhhhh..eeeeee....hhhhhh...hhhhhhhhhhhhhhhhhhh...eeee...........eeeee.....eeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeee.................hhhhhhhhhhhh....eeeeeehhhhh.....hhhhhhhhhh..eeeee...eee......eee........hhhhhhhhhhhhhhhhhhhh......ee......hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eay C  -1 SHMEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSVVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGLPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRSTMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR 394
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388      


Chain D from PDB  Type:PROTEIN  Length:395
                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee........hhhhhhhhh..eeee...........hhhhhhhhhhhhhhh..eeeeee....hhhhhhh..hhhhhhhhhhhhhhhhhhh...eeee...........eeeee.....eeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.eeee.................hhhhhhhhhhhh....eeeeeehhhhh.....hhhhhhhhhh..eeeee..eeee......eeee.......hhhhhhhhhhhhhhhhhhh.......ee......hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eay D  -1 SHMEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSVVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGLPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRSTMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFS 393
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388
   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 4EAY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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 Related Entries

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

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        UXUA_ECOLI | P24215: 4eac

(-) Related Entries Specified in the PDB File

1tz9 SEQUENCE HOMOLOGOUS
3dbn SEQUENCE HOMOLOGOUS
3fvm SEQUENCE HOMOLOGOUS
4eac