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(-) Description

Title :  1.63 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF DEHYDROGENASE (MVIM) FROM CLOSTRIDIUM DIFFICILE.
 
Authors :  G. Minasov, Z. Wawrzak, M. Kudritska, S. Grimshaw, L. Papazisi, A. Savc W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  28 Nov 11  (Deposition) - 21 Dec 11  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, Z. Wawrzak, M. Kudritska, S. Grimshaw, L. Papazisi, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 63 Angstrom Resolution Crystal Structure Of Dehydrogenase (Mvim) From Clostridium Difficile.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE WITH NAD(P)-BINDING ROSSMANN-FOLD DOMAIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CD630_34500, MVIM
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Strain: 630

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric/Biological Unit (5, 23)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CL13Ligand/IonCHLORIDE ION
3GOL4Ligand/IonGLYCEROL
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:259 , ILE A:260 , ASN C:259 , ILE C:260BINDING SITE FOR RESIDUE CL A 306
02AC2SOFTWAREGLY A:255 , ALA A:256 , TRP A:257 , HOH A:991 , HOH A:1197BINDING SITE FOR RESIDUE CL A 307
03AC3SOFTWAREARG A:124 , TRP A:174 , ALA A:284 , GOL A:310 , HOH A:544 , HOH A:1198BINDING SITE FOR RESIDUE CL A 308
04AC4SOFTWARETHR A:36 , ASN A:38 , LYS A:41BINDING SITE FOR RESIDUE CL A 309
05AC5SOFTWAREARG A:124 , PHE A:125 , LYS A:130 , TRP A:174 , CL A:308 , HOH A:544 , GLU B:278 , ASN B:279 , ASN B:280BINDING SITE FOR RESIDUE GOL A 310
06AC6SOFTWARECYS A:145 , HIS A:147 , SER A:212 , LEU A:221 , 1PE A:312 , SER B:141 , ASN B:143 , GLU B:225 , LEU B:227 , ARG B:234BINDING SITE FOR RESIDUE PEG A 311
07AC7SOFTWAREASN A:143 , SER A:199 , HIS A:200 , LYS A:201 , ASN A:210 , THR A:211 , SER A:212 , PEG A:311 , HOH A:348 , HOH A:718 , ASN B:143 , SER B:199 , HIS B:200 , ASN B:210 , THR B:211 , SER B:212 , HOH B:338BINDING SITE FOR RESIDUE 1PE A 312
08AC8SOFTWAREASN B:259 , ILE B:260 , ASN D:259 , ILE D:260BINDING SITE FOR RESIDUE CL B 306
09AC9SOFTWAREGLY B:255 , ALA B:256 , TRP B:257 , HOH B:799BINDING SITE FOR RESIDUE CL B 307
10BC1SOFTWARETHR B:36 , PRO B:37 , ASN B:38 , LYS B:41 , HOH B:785BINDING SITE FOR RESIDUE CL B 308
11BC2SOFTWAREGLU A:278 , ASN A:279 , ARG B:124 , PHE B:125 , LYS B:130 , TRP B:174 , HOH B:318 , HOH B:722BINDING SITE FOR RESIDUE GOL B 309
12BC3SOFTWAREILE B:14 , SER B:71 , THR B:73 , HIS B:76 , ASP B:93 , LYS B:94 , HOH B:490BINDING SITE FOR RESIDUE PEG B 310
13BC4SOFTWAREGLY C:255 , ALA C:256 , TRP C:257 , HOH C:456 , HOH C:1126BINDING SITE FOR RESIDUE CL C 306
14BC5SOFTWAREASN C:135 , GLN C:233 , HOH C:339 , HOH C:451BINDING SITE FOR RESIDUE CL C 307
15BC6SOFTWARETHR C:36 , PRO C:37 , ASN C:38BINDING SITE FOR RESIDUE CL C 308
16BC7SOFTWAREARG C:124 , PHE C:125 , LYS C:130 , TRP C:174 , HOH C:321 , HOH C:474 , ASN D:279BINDING SITE FOR RESIDUE GOL C 309
17BC8SOFTWARETRP A:257 , ASP C:93 , LYS C:94 , ASN C:122 , ARG C:123 , HIS C:167 , PHE C:266 , HOH C:340 , HOH C:343 , HOH C:606BINDING SITE FOR RESIDUE PGE C 310
18BC9SOFTWAREPHE C:197 , SER C:199 , HIS C:200 , ASN C:210 , THR C:211 , SER C:212 , HOH C:361 , SER D:141 , ASN D:143 , ASN D:210 , LEU D:227 , PEG D:310 , HOH D:385BINDING SITE FOR RESIDUE PEG C 311
19CC1SOFTWAREGLY D:255 , ALA D:256 , TRP D:257 , HOH D:1044BINDING SITE FOR RESIDUE CL D 306
20CC2SOFTWARETHR D:36 , PRO D:37 , ASN D:38BINDING SITE FOR RESIDUE CL D 307
21CC3SOFTWAREARG D:124 , GOL D:309BINDING SITE FOR RESIDUE CL D 308
22CC4SOFTWAREASN C:279 , ASN C:280 , ARG D:124 , PHE D:125 , LYS D:130 , TRP D:174 , CL D:308 , HOH D:882BINDING SITE FOR RESIDUE GOL D 309
23CC5SOFTWAREASN C:143 , LYS C:201 , ASN C:210 , PEG C:311 , ASN D:143 , SER D:199 , HIS D:200 , ASN D:210 , THR D:211 , HOH D:352BINDING SITE FOR RESIDUE PEG D 310

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:94 -Pro A:95
2Lys B:94 -Pro B:95
3Lys C:94 -Pro C:95
4Lys D:94 -Pro D:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UUW)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:304
 aligned with Q180U8_PEPD6 | Q180U8 from UniProtKB/TrEMBL  Length:305

    Alignment length:304
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    
         Q180U8_PEPD6     2 KNIKMGMIGLGSIAQKAYLPILTKSERFEFVGAFTPNKVKREKICSDYRIMPFDSIESLAKKCDCIFLHSSTETHYEIIKILLNLGVHVYVDKPLASTVSQGEELIELSTKKNLNLMVGFNRRFCPMYKEIKNNATEIVSINICKHGLNSLRNVRFDSTLIDDYIHVIDTALWLANEDVEISGEDLFLTDNKNLIFVSHKLKGKNFSINTSMHRDSGTKLEQVEILSKGKIQRVKNLNVLEIEEGGNLTLKQSGAWVNILKQKGFEDISNHFIDCIENNIKPAINGEECIKAQRLLEKIINSVK 305
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh.....hhhhhhh...eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh..eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeeee....eeeeeee......eeeeeeee..eeeeee...eeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uuw A   2 KNIKMGMIGLGSIAQKAYLPILTKSERFEFVGAFTPNKVKREKICSDYRIMPFDSIESLAKKCDCIFLHSSTETHYEIIKILLNLGVHVYVDKPLASTVSQGEELIELSTKKNLNLMVGFNRRFCPMYKEIKNNATEIVSINICKHGLNSLRNVRFDSTLIDDYIHVIDTALWLANEDVEISGEDLFLTDNKNLIFVSHKLKGKNFSINTSMHRDSGTKLEQVEILSKGKIQRVKNLNVLEIEEGGNLTLKQSGAWVNILKQKGFEDISNHFIDCIENNIKPAINGEECIKAQRLLEKIINSVK 305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with Q180U8_PEPD6 | Q180U8 from UniProtKB/TrEMBL  Length:305

    Alignment length:303
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   
         Q180U8_PEPD6     2 KNIKMGMIGLGSIAQKAYLPILTKSERFEFVGAFTPNKVKREKICSDYRIMPFDSIESLAKKCDCIFLHSSTETHYEIIKILLNLGVHVYVDKPLASTVSQGEELIELSTKKNLNLMVGFNRRFCPMYKEIKNNATEIVSINICKHGLNSLRNVRFDSTLIDDYIHVIDTALWLANEDVEISGEDLFLTDNKNLIFVSHKLKGKNFSINTSMHRDSGTKLEQVEILSKGKIQRVKNLNVLEIEEGGNLTLKQSGAWVNILKQKGFEDISNHFIDCIENNIKPAINGEECIKAQRLLEKIINSV 304
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh.....hhhhhhh...eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh..eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeeee....eeeeeee......eeeeeeee..eeeeee...eeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uuw B   2 KNIKMGMIGLGSIAQKAYLPILTKSERFEFVGAFTPNKVKREKICSDYRIMPFDSIESLAKKCDCIFLHSSTETHYEIIKILLNLGVHVYVDKPLASTVSQGEELIELSTKKNLNLMVGFNRRFCPMYKEIKNNATEIVSINICKHGLNSLRNVRFDSTLIDDYIHVIDTALWLANEDVEISGEDLFLTDNKNLIFVSHKLKGKNFSINTSMHRDSGTKLEQVEILSKGKIQRVKNLNVLEIEEGGNLTLKQSGAWVNILKQKGFEDISNHFIDCIENNIKPAINGEECIKAQRLLEKIINSV 304
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   


Chain C from PDB  Type:PROTEIN  Length:303
 aligned with Q180U8_PEPD6 | Q180U8 from UniProtKB/TrEMBL  Length:305

    Alignment length:303
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   
         Q180U8_PEPD6     2 KNIKMGMIGLGSIAQKAYLPILTKSERFEFVGAFTPNKVKREKICSDYRIMPFDSIESLAKKCDCIFLHSSTETHYEIIKILLNLGVHVYVDKPLASTVSQGEELIELSTKKNLNLMVGFNRRFCPMYKEIKNNATEIVSINICKHGLNSLRNVRFDSTLIDDYIHVIDTALWLANEDVEISGEDLFLTDNKNLIFVSHKLKGKNFSINTSMHRDSGTKLEQVEILSKGKIQRVKNLNVLEIEEGGNLTLKQSGAWVNILKQKGFEDISNHFIDCIENNIKPAINGEECIKAQRLLEKIINSV 304
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh.....hhhhhhh...eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh..eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeeee....eeeeeee......eeeeeeee..eeeeee...eeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uuw C   2 KNIKMGMIGLGSIAQKAYLPILTKSERFEFVGAFTPNKVKREKICSDYRIMPFDSIESLAKKCDCIFLHSSTETHYEIIKILLNLGVHVYVDKPLASTVSQGEELIELSTKKNLNLMVGFNRRFCPMYKEIKNNATEIVSINICKHGLNSLRNVRFDSTLIDDYIHVIDTALWLANEDVEISGEDLFLTDNKNLIFVSHKLKGKNFSINTSMHRDSGTKLEQVEILSKGKIQRVKNLNVLEIEEGGNLTLKQSGAWVNILKQKGFEDISNHFIDCIENNIKPAINGEECIKAQRLLEKIINSV 304
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   


Chain D from PDB  Type:PROTEIN  Length:303
 aligned with Q180U8_PEPD6 | Q180U8 from UniProtKB/TrEMBL  Length:305

    Alignment length:303
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   
         Q180U8_PEPD6     2 KNIKMGMIGLGSIAQKAYLPILTKSERFEFVGAFTPNKVKREKICSDYRIMPFDSIESLAKKCDCIFLHSSTETHYEIIKILLNLGVHVYVDKPLASTVSQGEELIELSTKKNLNLMVGFNRRFCPMYKEIKNNATEIVSINICKHGLNSLRNVRFDSTLIDDYIHVIDTALWLANEDVEISGEDLFLTDNKNLIFVSHKLKGKNFSINTSMHRDSGTKLEQVEILSKGKIQRVKNLNVLEIEEGGNLTLKQSGAWVNILKQKGFEDISNHFIDCIENNIKPAINGEECIKAQRLLEKIINSV 304
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh.....hhhhhhh...eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhh..eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeeee....eeeeeee......eeeeeeee..eeeeee...eeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uuw D   2 KNIKMGMIGLGSIAQKAYLPILTKSERFEFVGAFTPNKVKREKICSDYRIMPFDSIESLAKKCDCIFLHSSTETHYEIIKILLNLGVHVYVDKPLASTVSQGEELIELSTKKNLNLMVGFNRRFCPMYKEIKNNATEIVSINICKHGLNSLRNVRFDSTLIDDYIHVIDTALWLANEDVEISGEDLFLTDNKNLIFVSHKLKGKNFSINTSMHRDSGTKLEQVEILSKGKIQRVKNLNVLEIEEGGNLTLKQSGAWVNILKQKGFEDISNHFIDCIENNIKPAINGEECIKAQRLLEKIINSV 304
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
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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 3UUW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UUW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UUW)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q180U8_PEPD6 | Q180U8)
molecular function
    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.
biological process
    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.

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