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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF THE MG-BOUND 3-KETO-L-GULONATE-6-PHOSPHATE DECARBOXYLASE FROM VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961
 
Authors :  B. Nocek, N. Maltseva, J. Stam, W. Anderson, A. Joachimiak, Csgid
Date :  08 Sep 09  (Deposition) - 13 Oct 09  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  3-Keto-L-Gulonate-6-Phosphate Decarboxylase, Ulad, Csgid, Mg-Bound, Biosynthetic Protein, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, N. Maltseva, J. Stam, W. Anderson, A. Joachimiak, Csgid
Crystal Structure Of The Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEXULOSE-6-PHOSPHATE SYNTHASE SGBH
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PMCSG19C
    Gene: VC_A0242
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: N16961

 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  (5, 49)

Asymmetric Unit (5, 49)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GOL5Ligand/IonGLYCEROL
3MG7Ligand/IonMAGNESIUM ION
4MSE24Mod. Amino AcidSELENOMETHIONINE
5SO48Ligand/IonSULFATE ION
Biological Unit 1 (4, 21)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL3Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4MSE12Mod. Amino AcidSELENOMETHIONINE
5SO44Ligand/IonSULFATE ION
Biological Unit 2 (4, 21)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4MSE12Mod. Amino AcidSELENOMETHIONINE
5SO44Ligand/IonSULFATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:113 , TYR A:135 , HIS A:136 , HOH A:231BINDING SITE FOR RESIDUE EDO A 901
02AC2SOFTWAREALA A:88 , ALA A:90 , ILE A:95 , ASP A:121 , TRP A:125 , HOH A:246 , HOH A:469 , HOH A:724BINDING SITE FOR RESIDUE GOL A 1001
03AC3SOFTWARETHR A:118 , MSE A:119 , GLN A:120BINDING SITE FOR RESIDUE GOL A 1002
04AC4SOFTWAREARG A:51 , PRO A:55 , HIS A:57 , ASP A:82 , HOH A:498 , HOH A:687BINDING SITE FOR RESIDUE GOL A 1003
05AC5SOFTWAREASN A:56 , HOH A:245 , HOH A:743BINDING SITE FOR RESIDUE EDO A 902
06AC6SOFTWAREASP A:67 , GLY A:68 , GLY A:69 , ALA A:70 , THR A:94 , ALA A:97 , HOH A:227 , HOH A:271 , ARG B:139BINDING SITE FOR RESIDUE SO4 A 501
07AC7SOFTWAREGLY A:170 , GLY A:171 , ALA A:190 , GLY A:191 , HOH A:242 , HOH A:331 , HOH A:382 , HOH A:459 , HOH A:483 , HOH A:681BINDING SITE FOR RESIDUE SO4 A 502
08AC8SOFTWAREGLU A:33 , ASP A:62 , GLU A:112 , HOH A:249 , HOH A:258 , HOH A:284 , HOH A:285BINDING SITE FOR RESIDUE MG A 3001
09AC9SOFTWAREHOH A:275 , HOH A:790 , HOH A:791 , HOH A:792 , HOH A:793 , HOH A:794BINDING SITE FOR RESIDUE MG A 3002
10BC1SOFTWAREARG A:139 , ASP B:67 , GLY B:68 , GLY B:69 , ALA B:70 , THR B:94 , ALA B:97 , HOH B:242 , HOH B:467 , HOH B:479 , HOH B:503 , HOH B:553BINDING SITE FOR RESIDUE SO4 B 501
11BC2SOFTWAREGLY B:171 , ALA B:190 , GLY B:191 , HOH B:220 , HOH B:258 , HOH B:269 , HOH B:337 , HOH B:355 , HOH B:435BINDING SITE FOR RESIDUE SO4 B 502
12BC3SOFTWAREGLU B:33 , ASP B:62 , GLU B:112 , HOH B:239 , HOH B:249 , HOH B:302 , HOH B:304BINDING SITE FOR RESIDUE MG B 3001
13BC4SOFTWAREHIS B:52 , HOH B:531 , HOH B:774 , HOH B:775 , HOH C:266 , HOH C:505BINDING SITE FOR RESIDUE MG B 3002
14BC5SOFTWAREALA C:88 , ALA C:90 , ILE C:92 , ILE C:95 , ASP C:121 , TRP C:125 , HOH C:264BINDING SITE FOR RESIDUE EDO C 901
15BC6SOFTWAREARG C:212BINDING SITE FOR RESIDUE EDO C 902
16BC7SOFTWAREASP C:67 , GLY C:68 , GLY C:69 , ALA C:70 , ALA C:93 , THR C:94 , ALA C:97 , HOH C:229 , HOH C:438 , HOH C:639 , HOH C:642 , ARG D:139BINDING SITE FOR RESIDUE SO4 C 501
17BC8SOFTWAREGLY C:170 , GLY C:171 , ALA C:190 , GLY C:191 , HOH C:217 , HOH C:396 , HOH C:474 , HOH C:500 , HOH C:694BINDING SITE FOR RESIDUE SO4 C 502
18BC9SOFTWARETHR C:13 , ASN C:14BINDING SITE FOR RESIDUE SO4 C 503
19CC1SOFTWAREHIS C:136 , HOH C:269 , HOH C:272 , HOH C:273 , HOH C:274 , HOH C:276BINDING SITE FOR RESIDUE MG C 3002
20CC2SOFTWAREGLU C:33 , ASP C:62 , GLU C:112 , HOH C:230 , HOH C:255 , HOH C:258 , HOH C:271BINDING SITE FOR RESIDUE MG C 3001
21CC3SOFTWAREILE D:113 , TYR D:135 , HIS D:136 , SER D:138 , HOH D:221 , HOH D:231BINDING SITE FOR RESIDUE GOL D 1001
22CC4SOFTWAREARG C:139 , HOH C:269 , ASP D:67 , GLY D:68 , GLY D:69 , ALA D:70 , THR D:94 , HOH D:708BINDING SITE FOR RESIDUE GOL D 1002
23CC5SOFTWAREALA D:88 , ALA D:90 , TRP D:125BINDING SITE FOR RESIDUE EDO D 901
24CC6SOFTWAREGLY D:170 , GLY D:171 , ALA D:190 , GLY D:191 , HOH D:236 , HOH D:380 , HOH D:395 , HOH D:582BINDING SITE FOR RESIDUE SO4 D 501
25CC7SOFTWAREGLU D:33 , ASP D:62 , HOH D:248 , HOH D:249 , HOH D:250 , HOH D:251BINDING SITE FOR RESIDUE MG D 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JR2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp B:214 -Pro B:215
2Trp C:214 -Pro C:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JR2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JR2)

(-) Exons   (0, 0)

(no "Exon" information available for 3JR2)

(-) 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:213
 aligned with Q9KMS8_VIBCH | Q9KMS8 from UniProtKB/TrEMBL  Length:215

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         Q9KMS8_VIBCH     2 TKPMIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGMKAVSTLRHNHPNHILVCDMKTTDGGAILSRMAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTMQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKMRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFW 214
               SCOP domains d3jr2a_ A: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains 3jr2A00 A:2-214 Aldolase class I                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhh...eeeee.hhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jr2 A   2 TKPmIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGmKAVSTLRHNHPNHILVCDmKTTDGGAILSRmAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTmQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKmRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFW 214
                               |    11        21        31        41  |     51        61 |      71   |    81        91       101       111       121       131       141       151    |  161       171       181       191       201       211   
                               |                                     44-MSE             63-MSE      75-MSE                                     119-MSE                              156-MSE                                                      
                               5-MSE                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q9KMS8_VIBCH | Q9KMS8 from UniProtKB/TrEMBL  Length:215

    Alignment length:213
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   
         Q9KMS8_VIBCH     3 KPMIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGMKAVSTLRHNHPNHILVCDMKTTDGGAILSRMAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTMQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKMRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
               SCOP domains d3jr2b_ B: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains 3jr2B00 B:3-215 Aldolase class I                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh...eeeee.hhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jr2 B   3 KPmIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGmKAVSTLRHNHPNHILVCDmKTTDGGAILSRmAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTmQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKmRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
                              |     12        22        32        42 |      52        62|       72  |     82        92       102       112      |122       132       142       152   |   162       172       182       192       202       212   
                              5-MSE                                 44-MSE             63-MSE      75-MSE                                     119-MSE                              156-MSE                                                       


Chain C from PDB  Type:PROTEIN  Length:214
 aligned with Q9KMS8_VIBCH | Q9KMS8 from UniProtKB/TrEMBL  Length:215

    Alignment length:214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
         Q9KMS8_VIBCH     2 TKPMIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGMKAVSTLRHNHPNHILVCDMKTTDGGAILSRMAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTMQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKMRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
               SCOP domains d3jr2c_ C: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 3jr2C00 C:2-215 Aldolase class I                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh...eeeee.hhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jr2 C   2 TKPmIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGmKAVSTLRHNHPNHILVCDmKTTDGGAILSRmAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTmQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKmRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
                               |    11        21        31        41  |     51        61 |      71   |    81        91       101       111       121       131       141       151    |  161       171       181       191       201       211    
                               5-MSE                                 44-MSE             63-MSE      75-MSE                                     119-MSE                              156-MSE                                                       


Chain D from PDB  Type:PROTEIN  Length:212
 aligned with Q9KMS8_VIBCH | Q9KMS8 from UniProtKB/TrEMBL  Length:215

    Alignment length:212
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  
         Q9KMS8_VIBCH     3 KPMIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGMKAVSTLRHNHPNHILVCDMKTTDGGAILSRMAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTMQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKMRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFW 214
               SCOP domains d3jr2d_ D: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 3jr2D00 D:3-214 Aldolase class I                                                                                                                                                                                     CATH domains
           Pfam domains (1) -OMPdecase-3jr2D01 D:4-207                                                                                                                                                                                   ------- Pfam domains (1)
           Pfam domains (2) -OMPdecase-3jr2D02 D:4-207                                                                                                                                                                                   ------- Pfam domains (2)
           Pfam domains (3) -OMPdecase-3jr2D03 D:4-207                                                                                                                                                                                   ------- Pfam domains (3)
           Pfam domains (4) -OMPdecase-3jr2D04 D:4-207                                                                                                                                                                                   ------- Pfam domains (4)
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh...eeeee.hhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jr2 D   3 KPmIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGmKAVSTLRHNHPNHILVCDmKTTDGGAILSRmAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTmQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKmRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFW 214
                              |     12        22        32        42 |      52        62|       72  |     82        92       102       112      |122       132       142       152   |   162       172       182       192       202       212  
                              5-MSE                                 44-MSE             63-MSE      75-MSE                                     119-MSE                              156-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9KMS8_VIBCH | Q9KMS8)
molecular function
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    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:0004590    orotidine-5'-phosphate decarboxylase activity    Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
biological process
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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        Q9KMS8_VIBCH | Q9KMS8: 3ieb

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3ieb RELATED ID: IDP01486 RELATED DB: TARGETDB