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(-) Description

Title :  CRYSTAL STRUCTURE OF A NITROREDUCTASE FAMILY PROTEIN (CD3355) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.58 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  13 Nov 09  (Deposition) - 01 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Nitroreductase Family Protein (Yp_001089872. 1) From Clostridium Difficile 630 At 1. 58 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NITROREDUCTASE FAMILY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CD3355
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Strain: 630

 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  (4, 35)

Asymmetric Unit (4, 35)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL13Ligand/IonGLYCEROL
4MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 17)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL7Ligand/IonGLYCEROL
4MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL6Ligand/IonGLYCEROL
4MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:10 , TYR A:11 , SER A:12 , ARG A:14 , TYR A:66 , VAL A:115 , TRP A:116 , VAL A:117 , CYS A:118 , TYR A:119 , ARG A:155 , ARG A:160 , HOH A:242 , HOH A:330 , HOH A:490 , HOH A:636 , PRO B:37 , THR B:38 , GLY B:39 , ASN B:41 , ILE B:94 , ASP B:95 , ILE B:98 , CL B:173 , LYS C:148 , HOH C:284BINDING SITE FOR RESIDUE FMN A 300
02AC2SOFTWARELYS A:9 , PRO A:150 , HOH A:653 , HOH A:680 , HOH A:708BINDING SITE FOR RESIDUE GOL A 173
03AC3SOFTWAREGLY A:40 , TRP A:82 , HOH A:881 , GOL B:176 , FMN B:300BINDING SITE FOR RESIDUE GOL A 174
04AC4SOFTWAREILE A:149 , PRO A:150 , GLU A:151BINDING SITE FOR RESIDUE GOL A 175
05AC5SOFTWAREMSE A:1 , ASN A:2 , PHE A:3 , GLU A:109 , MSE B:1 , PHE B:3 , LEU B:6 , GLU B:109BINDING SITE FOR RESIDUE GOL A 176
06AC6SOFTWAREPRO A:37 , THR A:38 , GLY A:39 , ASN A:41 , ILE A:94 , ASP A:95 , ILE A:98 , GOL A:174 , ARG B:10 , TYR B:11 , SER B:12 , ARG B:14 , TYR B:66 , VAL B:115 , TRP B:116 , VAL B:117 , CYS B:118 , TYR B:119 , ARG B:155 , ARG B:160 , GOL B:176 , HOH B:197 , HOH B:233 , HOH B:247BINDING SITE FOR RESIDUE FMN B 300
07AC7SOFTWAREFMN A:300 , GLY B:40 , ILE C:149BINDING SITE FOR RESIDUE CL B 173
08AC8SOFTWAREILE B:149 , HOH B:779 , GLY C:40 , FMN D:300BINDING SITE FOR RESIDUE CL B 174
09AC9SOFTWAREPHE A:86 , ALA B:62 , ASN B:64 , TYR B:119 , HOH B:195 , HOH B:229BINDING SITE FOR RESIDUE GOL B 175
10BC1SOFTWAREGOL A:174 , HOH A:881 , ARG B:14 , FMN B:300 , HOH B:716 , HOH B:789BINDING SITE FOR RESIDUE GOL B 176
11BC2SOFTWARETYR A:119 , HOH A:434 , HOH A:577 , ARG B:84 , PRO B:85 , PHE B:86BINDING SITE FOR RESIDUE GOL B 177
12BC3SOFTWAREARG C:10 , TYR C:11 , SER C:12 , ARG C:14 , TYR C:66 , VAL C:115 , TRP C:116 , VAL C:117 , CYS C:118 , TYR C:119 , ARG C:155 , ARG C:160 , HOH C:264 , HOH C:336 , HOH C:709 , PRO D:37 , THR D:38 , GLY D:39 , ASN D:41 , ILE D:94 , ILE D:98 , GOL D:175BINDING SITE FOR RESIDUE FMN C 300
13BC4SOFTWAREALA C:62 , ASN C:64 , TYR C:119 , HOH C:311 , HOH C:769 , PHE D:86BINDING SITE FOR RESIDUE GOL C 173
14BC5SOFTWARELYS C:9 , THR C:108 , GLY C:111 , LEU C:112 , ALA C:113 , GLU C:146 , PRO C:150 , HOH C:237 , HOH C:371 , HOH C:414BINDING SITE FOR RESIDUE GOL C 174
15BC6SOFTWARELYS C:158 , THR C:159 , ARG C:160 , VAL C:161 , ASN D:41 , GLN D:43BINDING SITE FOR RESIDUE GOL C 175
16BC7SOFTWARELYS B:148 , CL B:174 , PRO C:37 , THR C:38 , GLY C:39 , ASN C:41 , LEU C:91 , ILE C:94 , ILE C:98 , ARG D:10 , TYR D:11 , SER D:12 , ARG D:14 , TYR D:66 , VAL D:115 , TRP D:116 , VAL D:117 , CYS D:118 , TYR D:119 , ARG D:155 , ARG D:160 , HOH D:241 , HOH D:280 , HOH D:356 , HOH D:365 , HOH D:654BINDING SITE FOR RESIDUE FMN D 300
17BC8SOFTWARELYS D:9 , PRO D:150 , HOH D:341 , HOH D:580 , HOH D:762BINDING SITE FOR RESIDUE GOL D 173
18BC9SOFTWAREMSE C:1 , GLU C:109 , MSE D:1 , ASN D:2 , GLU D:109BINDING SITE FOR RESIDUE GOL D 174
19CC1SOFTWARETYR C:119 , FMN C:300 , GLY D:40 , TRP D:82BINDING SITE FOR RESIDUE GOL D 175

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KOQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KOQ)

(-) 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:173
 aligned with Q180K0_PEPD6 | Q180K0 from UniProtKB/TrEMBL  Length:172

    Alignment length:173
                             1                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169   
         Q180K0_PEPD6     - -MNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHMMLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLMGYESKIPESPERHEKTRVPLSEIVSYETL 172
               SCOP domains d3koqa_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...........hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhh......eeeeeeee.............hhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh.....eeeeeeeeee..........hhhhhh.hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3koq A   0 GmNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHmmLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLmGYESKIPESPERHEKTRVPLSEIVSYETL 172
                             |       9        19        29        39        49        59        69        79        89        99   ||  109       119       129       139   |   149       159       169   
                             |                                                                                                   103-MSE                                 143-MSE                         
                             1-MSE                                                                                                104-MSE                                                                


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with Q180K0_PEPD6 | Q180K0 from UniProtKB/TrEMBL  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
         Q180K0_PEPD6     1 MNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHMMLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLMGYESKIPESPERHEKTRVPLSEIVSYETL 172
               SCOP domains d3koqb_ B: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...........hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhh......eeeeeeee.............hhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh.....eeeeeeeeee..........hhhhhh.hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3koq B   1 mNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHmmLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLmGYESKIPESPERHEKTRVPLSEIVSYETL 172
                            |       10        20        30        40        50        60        70        80        90       100  ||   110       120       130       140  |    150       160       170  
                            1-MSE                                                                                               103-MSE                                 143-MSE                         
                                                                                                                                 104-MSE                                                                


Chain C from PDB  Type:PROTEIN  Length:172
 aligned with Q180K0_PEPD6 | Q180K0 from UniProtKB/TrEMBL  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
         Q180K0_PEPD6     1 MNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHMMLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLMGYESKIPESPERHEKTRVPLSEIVSYETL 172
               SCOP domains d3koqc_ C: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...........hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhh......eeeeeeee.............hhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh.....eeeeeeeeee..........hhhhhh.hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3koq C   1 mNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHmmLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLmGYESKIPESPERHEKTRVPLSEIVSYETL 172
                            |       10        20        30        40        50        60        70        80        90       100  ||   110       120       130       140  |    150       160       170  
                            1-MSE                                                                                               103-MSE                                 143-MSE                         
                                                                                                                                 104-MSE                                                                


Chain D from PDB  Type:PROTEIN  Length:172
 aligned with Q180K0_PEPD6 | Q180K0 from UniProtKB/TrEMBL  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
         Q180K0_PEPD6     1 MNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHMMLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLMGYESKIPESPERHEKTRVPLSEIVSYETL 172
               SCOP domains d3koqd_ D: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...........hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhh........eeeeeeee.............hhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh.....eeeeeeeeee..........hhhhhh.hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3koq D   1 mNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHmmLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLmGYESKIPESPERHEKTRVPLSEIVSYETL 172
                            |       10        20        30        40        50        60        70        80        90       100  ||   110       120       130       140  |    150       160       170  
                            1-MSE                                                                                               103-MSE                                 143-MSE                         
                                                                                                                                 104-MSE
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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) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q180K0_PEPD6 | Q180K0)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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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        Q180K0_PEPD6 | Q180K0: 3h4o

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