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(-) Description

Title :  CRYSTAL STRUCTURE OF THE A314P MUTANT OF MANNONATE DEHYDRATASE FROM NOVOSPHINGOBIUM AROMATICIVORANS COMPLEXED WITH MG AND D-MANNONATE
 
Authors :  A. A. Fedorov, E. V. Fedorov, D. Wichelecki, J. A. Gerlt, S. C. Almo
Date :  06 Apr 13  (Deposition) - 09 Apr 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Enolase Fold, Mannonate Dehydratase, D-Mannonate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, D. Wichelecki, J. A. Gerlt, S. C. Almo
Crystal Structure Of The A314P Mutant Of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed With Mg And D-Mannonate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME, N-TERMINAL DOMAIN PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SARO_3675
    Mutation: YES
    Organism Scientific: NOVOSPHINGOBIUM AROMATICIVORANS
    Organism Taxid: 279238
    Strain: DSM 12444

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 23)

Asymmetric Unit (6, 23)
No.NameCountTypeFull Name
1CO25Ligand/IonCARBON DIOXIDE
2CO31Ligand/IonCARBONATE ION
3CS24Ligand/IonD-MANNONIC ACID
4MG5Ligand/IonMAGNESIUM ION
5PDO4Ligand/Ion1,3-PROPANDIOL
6PGE4Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1CO22Ligand/IonCARBON DIOXIDE
2CO3-1Ligand/IonCARBONATE ION
3CS22Ligand/IonD-MANNONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5PDO2Ligand/Ion1,3-PROPANDIOL
6PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (5, 10)
No.NameCountTypeFull Name
1CO23Ligand/IonCARBON DIOXIDE
2CO31Ligand/IonCARBONATE ION
3CS22Ligand/IonD-MANNONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5PDO2Ligand/Ion1,3-PROPANDIOL
6PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:210 , GLU A:236 , GLU A:262 , CS2 A:502 , HOH A:848BINDING SITE FOR RESIDUE MG A 501
02AC2SOFTWAREASN A:37 , HIS A:122 , ARG A:147 , ASP A:210 , HIS A:212 , GLU A:236 , GLU A:262 , ARG A:283 , HIS A:312 , PRO A:314 , ASP A:316 , GLU A:339 , LEU A:389 , TRP A:402 , MG A:501 , HOH A:634 , HOH A:848 , TYR B:75 , TRP B:76BINDING SITE FOR RESIDUE CS2 A 502
03AC3SOFTWARELYS A:192 , GLU A:195 , MET A:226 , TYR A:230BINDING SITE FOR RESIDUE PGE A 503
04AC4SOFTWAREARG A:78 , GLY A:79 , PRO A:80 , VAL A:81 , THR A:82 , GLY B:79 , PRO B:80 , VAL B:81 , THR B:82BINDING SITE FOR RESIDUE CO2 A 504
05AC5SOFTWAREGLU A:228 , PRO A:229 , GLN A:231 , HOH A:859 , HOH C:718BINDING SITE FOR RESIDUE CO2 A 505
06AC6SOFTWAREHIS A:209 , ASP A:210 , TYR A:215 , HOH A:758BINDING SITE FOR RESIDUE PDO A 506
07AC7SOFTWAREASP B:210 , GLU B:236 , GLU B:262 , CS2 B:502 , HOH B:856BINDING SITE FOR RESIDUE MG B 501
08AC8SOFTWARETYR A:75 , TRP A:76 , ASN B:37 , HIS B:122 , ARG B:147 , ASP B:210 , HIS B:212 , GLU B:236 , GLU B:262 , ARG B:283 , HIS B:312 , PRO B:314 , ASP B:316 , GLU B:339 , LEU B:389 , TRP B:402 , MG B:501 , HOH B:625 , HOH B:856BINDING SITE FOR RESIDUE CS2 B 502
09AC9SOFTWAREPRO B:191 , LYS B:192 , GLU B:195 , TYR B:230 , PHE D:203BINDING SITE FOR RESIDUE PGE B 503
10BC1SOFTWAREHOH B:874 , HOH B:882 , HOH B:883 , HOH D:812BINDING SITE FOR RESIDUE MG B 504
11BC2SOFTWAREHIS B:209 , ASP B:210 , GLY B:211 , TYR B:215 , HOH B:745BINDING SITE FOR RESIDUE PDO B 505
12BC3SOFTWAREASP C:210 , GLU C:236 , GLU C:262 , CS2 C:502 , HOH C:812BINDING SITE FOR RESIDUE MG C 501
13BC4SOFTWAREASN C:37 , HIS C:122 , ARG C:147 , ASP C:210 , HIS C:212 , GLU C:236 , GLU C:262 , ARG C:283 , HIS C:312 , PRO C:314 , ASP C:316 , GLU C:339 , LEU C:389 , TRP C:402 , MG C:501 , HOH C:613 , HOH C:812 , TYR D:75 , TRP D:76BINDING SITE FOR RESIDUE CS2 C 502
14BC5SOFTWAREPRO C:191 , LYS C:192 , GLU C:195 , TYR C:230BINDING SITE FOR RESIDUE PGE C 503
15BC6SOFTWAREARG C:78 , GLY C:79 , PRO C:80 , VAL C:81 , THR C:82 , GLY D:79 , PRO D:80 , VAL D:81 , THR D:82BINDING SITE FOR RESIDUE CO2 C 504
16BC7SOFTWAREARG C:297 , ALA C:299 , ASP C:300 , SER C:303 , PRO C:333 , ASN C:334BINDING SITE FOR RESIDUE CO2 C 505
17BC8SOFTWAREARG C:61 , MET C:103 , HOH C:682 , HOH C:776BINDING SITE FOR RESIDUE CO3 C 506
18BC9SOFTWARETRP C:181 , HIS C:209 , ASP C:210 , TYR C:215BINDING SITE FOR RESIDUE PDO C 507
19CC1SOFTWAREASP D:210 , GLU D:236 , GLU D:262 , CS2 D:502 , HOH D:801BINDING SITE FOR RESIDUE MG D 501
20CC2SOFTWARETYR C:75 , ASN D:37 , HIS D:122 , ARG D:147 , ASP D:210 , HIS D:212 , GLU D:236 , GLU D:262 , ARG D:283 , HIS D:312 , PRO D:314 , ASP D:316 , GLU D:339 , LEU D:389 , TRP D:402 , MG D:501 , HOH D:621 , HOH D:801BINDING SITE FOR RESIDUE CS2 D 502
21CC3SOFTWAREASN D:188 , LYS D:192 , GLU D:195 , TYR D:230BINDING SITE FOR RESIDUE PGE D 503
22CC4SOFTWAREGLU C:245 , HOH C:612 , LYS D:271 , ASP D:272 , HOH D:637 , HOH D:707 , HOH D:820BINDING SITE FOR RESIDUE CO2 D 504
23CC5SOFTWAREHIS D:209 , GLY D:211 , TYR D:215BINDING SITE FOR RESIDUE PDO D 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K1W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K1W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K1W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K1W)

(-) Exons   (0, 0)

(no "Exon" information available for 4K1W)

(-) 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 ............eeeeeeeee.....eeeeeeee....eeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee..........eeeehhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh..eeeee....hhhhhhhh...eeee..eeee..........hhhhhh..........eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1w A  -9 SSGLVPRGSHMKITAARVIITCPGRNFVTLKIETDQGVYGIGDATLNGRELSVVAYLQEHVAPCLIGMDPRRIEDIWQYVYRGAYWRRGPVTMRAIAAVDMALWDIKAKMAGMPLYQLLGGRSRDGIMVYGHANGSDIAETVEAVGHYIDMGYKAIRAQTGVPGIKSLPSVTGWDTRKALNYVPKLFEELRKTYGFDHHLLHDGHHRYTPQEAANLGKMLEPYQLFWLEDCTPAENQEAFRLVRQHTVTPLAVGEIFNTIWDAKDLIQNQLIDYIRATVVGAGGLTHLRRIADLASLYQVRTGCHGPTDLSPVTMGCALHFDTWVPNFGIQEYMRHTEETDAVFPHDYWFEKGELFVGETPGHGVDIDEELAAKYPYKPAYLPVARLEDGTMWNW 402
                                     0        10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     ||177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397     
                                                                                                                                                                                               156|                                                                                                                                                                                                                                    
                                                                                                                                                                                                174                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....eeeeeeee....eeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee..........eeeehhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhh...eeee..eeee..........hhhhhh..........eeee....ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1w B   0 HMKITAARVIITCPGRNFVTLKIETDQGVYGIGDATLNGRELSVVAYLQEHVAPCLIGMDPRRIEDIWQYVYRGAYWRRGPVTMRAIAAVDMALWDIKAKMAGMPLYQLLGGRSRDGIMVYGHANGSDIAETVEAVGHYIDMGYKAIRAQTGVPGIKSLPSVTGWDTRKALNYVPKLFEELRKTYGFDHHLLHDGHHRYTPQEAANLGKMLEPYQLFWLEDCTPAENQEAFRLVRQHTVTPLAVGEIFNTIWDAKDLIQNQLIDYIRATVVGAGGLTHLRRIADLASLYQVRTGCHGPTDLSPVTMGCALHFDTWVPNFGIQEYMRHTEETDAVFPHDYWFEKGELFVGETPGHGVDIDEELAAKYPYKPAYLPVARLEDGTMWNW 402
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149      |176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396      
                                                                                                                                                                                      156|                                                                                                                                                                                                                                    
                                                                                                                                                                                       174                                                                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.....eeeeeeee....eeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee........eeeehhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhh...eeee..eeee..........hhhhhh..........eeee....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k1w C   0 HMKITAARVIITCPGRNFVTLKIETDQGVYGIGDATLNGRELSVVAYLQEHVAPCLIGMDPRRIEDIWQYVYRGAYWRRGPVTMRAIAAVDMALWDIKAKMAGMPLYQLLGGRSRDGIMVYGHANGSDIAETVEAVGHYIDMGYKAIRAQTGVPGILPSVTGWDTRKALNYVPKLFEELRKTYGFDHHLLHDGHHRYTPQEAANLGKMLEPYQLFWLEDCTPAENQEAFRLVRQHTVTPLAVGEIFNTIWDAKDLIQNQLIDYIRATVVGAGGLTHLRRIADLASLYQVRTGCHGPTDLSPVTMGCALHFDTWVPNFGIQEYMRHTEETDAVFPHDYWFEKGELFVGETPGHGVDIDEELAAKYPYKPAYLPVARLEDGTMWNW 402
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149     ||178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398    
                                                                                                                                                                                     155|                                                                                                                                                                                                                                   
                                                                                                                                                                                      175                                                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.....eeeeeeee....eeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee........eeeehhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhh....eee..eee...........hhhhhh..........eeee....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k1w D   0 HMKITAARVIITCPGRNFVTLKIETDQGVYGIGDATLNGRELSVVAYLQEHVAPCLIGMDPRRIEDIWQYVYRGAYWRRGPVTMRAIAAVDMALWDIKAKMAGMPLYQLLGGRSRDGIMVYGHANGSDIAETVEAVGHYIDMGYKAIRAQTGVPGILPSVTGWDTRKALNYVPKLFEELRKTYGFDHHLLHDGHHRYTPQEAANLGKMLEPYQLFWLEDCTPAENQEAFRLVRQHTVTPLAVGEIFNTIWDAKDLIQNQLIDYIRATVVGAGGLTHLRRIADLASLYQVRTGCHGPTDLSPVTMGCALHFDTWVPNFGIQEYMRHTEETDAVFPHDYWFEKGELFVGETPGHGVDIDEELAAKYPYKPAYLPVARLEDGTMWNW 402
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149     ||178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398    
                                                                                                                                                                                     155|                                                                                                                                                                                                                                   
                                                                                                                                                                                      175
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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 4K1W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K1W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K1W)

(-) Gene Ontology  (10, 10)

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        MAND_NOVAD | A4XF23: 2qjj 2qjm 2qjn 4k8g

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