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(-) Description

Title :  YFIT FROM BACILLUS SUBTILIS IS A PROBABLE METAL-DEPENDENT HYDROLASE WITH AN UNUSUAL FOUR-HELIX BUNDLE TOPOLOGY
 
Authors :  S. S. Rajan, X. Yang, W. F. Anderson, Midwest Center For Structural (Mcsg)
Date :  18 Dec 03  (Deposition) - 20 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,D  (1x)
Biol. Unit 3:  B,C  (1x)
Keywords :  Nickel-Binding, Hydrolase, Helix-Bundle, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Metal-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Rajan, X. Yang, L. Shuvalova, F. Collart, W. F. Anderson
Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase With An Unusual Four-Helix Bundle Topology
Biochemistry V. 43 15472 2004
PubMed-ID: 15581359  |  Reference-DOI: 10.1021/BI048665R

(-) Compounds

Molecule 1 - YFIT
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YFIT
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A  D
Biological Unit 3 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 22)

Asymmetric Unit (7, 22)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GLY1Mod. Amino AcidGLYCINE
4MSE12Mod. Amino AcidSELENOMETHIONINE
5NI4Ligand/IonNICKEL (II) ION
6SER2Mod. Amino AcidSERINE
7THR1Mod. Amino AcidTHREONINE
Biological Unit 1 (6, 18)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GLY1Mod. Amino AcidGLYCINE
4MSE12Mod. Amino AcidSELENOMETHIONINE
5NI-1Ligand/IonNICKEL (II) ION
6SER2Mod. Amino AcidSERINE
7THR1Mod. Amino AcidTHREONINE
Biological Unit 2 (6, 12)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GLY1Mod. Amino AcidGLYCINE
4MSE6Mod. Amino AcidSELENOMETHIONINE
5NI-1Ligand/IonNICKEL (II) ION
6SER2Mod. Amino AcidSERINE
7THR1Mod. Amino AcidTHREONINE
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1ALA-1Mod. Amino AcidALANINE
2GLU-1Mod. Amino AcidGLUTAMIC ACID
3GLY-1Mod. Amino AcidGLYCINE
4MSE6Mod. Amino AcidSELENOMETHIONINE
5NI-1Ligand/IonNICKEL (II) ION
6SER-1Mod. Amino AcidSERINE
7THR-1Mod. Amino AcidTHREONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:67 , HIS A:160 , HIS A:164 , HOH A:310 , HOH A:311 , HOH A:312BINDING SITE FOR RESIDUE NI A 300
02AC2SOFTWAREHIS B:67 , HIS B:160 , HIS B:164 , HOH B:311 , HOH B:312 , HOH B:313BINDING SITE FOR RESIDUE NI B 300
03AC3SOFTWAREHIS C:67 , HIS C:160 , HIS C:164 , HOH C:302 , HOH C:303 , HOH C:346BINDING SITE FOR RESIDUE NI C 300
04AC4SOFTWAREHIS D:67 , HIS D:160 , HIS D:164 , GLU D:501 , HOH D:623 , HOH D:624 , HOH D:625BINDING SITE FOR RESIDUE NI D 300
05AC5SOFTWARETRP D:59 , HIS D:67 , GLU D:95 , HIS D:160 , HIS D:164 , NI D:300 , SER D:502 , ALA D:503 , THR D:504 , HOH D:623 , HOH D:624 , HOH D:625 , HOH D:626BINDING SITE FOR RESIDUE GLU D 501
06AC6SOFTWARELEU D:156 , TYR D:157 , TRP D:159 , HIS D:160 , GLU D:501 , ALA D:503 , THR D:504 , HOH D:625BINDING SITE FOR RESIDUE SER D 502
07AC7SOFTWARELEU D:156 , GLU D:501 , SER D:502 , THR D:504BINDING SITE FOR RESIDUE ALA D 503
08AC8SOFTWAREILE C:10 , GLU D:501 , SER D:502 , ALA D:503 , SER D:505 , GLY D:506BINDING SITE FOR RESIDUE THR D 504
09AC9SOFTWAREGLY C:11 , GLU D:12 , THR D:504 , GLY D:506 , HOH D:627BINDING SITE FOR RESIDUE SER D 505
10BC1SOFTWAREASN C:5 , TYR C:8 , THR D:504 , SER D:505BINDING SITE FOR RESIDUE GLY D 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RXQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RXQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RXQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RXQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1RXQ)

(-) 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:174
 aligned with YFIT_BACSU | O31562 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    
           YFIT_BACSU     5 NLSYPIGEYKPRESISKEQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRFKLSLTEETPAIRPYDEKAWSELKDSKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGWS 178
               SCOP domains d1rxqa_ A: YfiT                                                                                                                                                                SCOP domains
               CATH domains 1rxqA00 A:5-178 dinb family like domain                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee......eeehhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rxq A   5 NLSYPIGEYKPRESISKEQKDKWIQVLEEVPAKLKQAVEVmTDSQLDTPYRDGGWTVRQVVHHLADSHmNSYIRFKLSLTEETPAIRPYDEKAWSELKDSKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKEIITLENALGLYVWHSHHHIAHITELSRRmGWS 178
                                    14        24        34        44|       54        64        74        84        94       104       114       124       134       144       154       164       174|   
                                                                   45-MSE                      73-MSE                                                                                               175-MSE


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with YFIT_BACSU | O31562 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:175
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173     
           YFIT_BACSU     4 VNLSYPIGEYKPRESISKEQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRFKLSLTEETPAIRPYDEKAWSELKDSKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGWS 178
               SCOP domains d1rxqb_ B: YfiT                                                                                                                                                                 SCOP domains
               CATH domains 1rxqB00 B:4-178 dinb family like domain                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee......eeehhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rxq B   4 VNLSYPIGEYKPRESISKEQKDKWIQVLEEVPAKLKQAVEVmTDSQLDTPYRDGGWTVRQVVHHLADSHmNSYIRFKLSLTEETPAIRPYDEKAWSELKDSKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKEIITLENALGLYVWHSHHHIAHITELSRRmGWS 178
                                    13        23        33        43 |      53        63        73        83        93       103       113       123       133       143       153       163       173 |   
                                                                    45-MSE                      73-MSE                                                                                               175-MSE


Chain C from PDB  Type:PROTEIN  Length:174
 aligned with YFIT_BACSU | O31562 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    
           YFIT_BACSU     5 NLSYPIGEYKPRESISKEQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRFKLSLTEETPAIRPYDEKAWSELKDSKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGWS 178
               SCOP domains d1rxqc_ C: YfiT                                                                                                                                                                SCOP domains
               CATH domains 1rxqC00 C:5-178 dinb family like domain                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhheee......eeehhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rxq C   5 NLSYPIGEYKPRESISKEQKDKWIQVLEEVPAKLKQAVEVmTDSQLDTPYRDGGWTVRQVVHHLADSHmNSYIRFKLSLTEETPAIRPYDEKAWSELKDSKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKEIITLENALGLYVWHSHHHIAHITELSRRmGWS 178
                                    14        24        34        44|       54        64        74        84        94       104       114       124       134       144       154       164       174|   
                                                                   45-MSE                      73-MSE                                                                                               175-MSE


Chain D from PDB  Type:PROTEIN  Length:169
 aligned with YFIT_BACSU | O31562 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:169
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           YFIT_BACSU    10 IGEYKPRESISKEQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRFKLSLTEETPAIRPYDEKAWSELKDSKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGWS 178
               SCOP domains d1rxqd_ D: YfiT                                                                                                                                                           SCOP domains
               CATH domains 1rxqD00 D:10-178 dinb family like domain                                                                                                                                  CATH domains
           Pfam domains (1) --------------------DinB_2-1rxqD01 D:30-168                                                                                                                    ---------- Pfam domains (1)
           Pfam domains (2) --------------------DinB_2-1rxqD02 D:30-168                                                                                                                    ---------- Pfam domains (2)
           Pfam domains (3) --------------------DinB_2-1rxqD03 D:30-168                                                                                                                    ---------- Pfam domains (3)
           Pfam domains (4) --------------------DinB_2-1rxqD04 D:30-168                                                                                                                    ---------- Pfam domains (4)
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rxq D  10 IGEYKPRESISKEQKDKWIQVLEEVPAKLKQAVEVmTDSQLDTPYRDGGWTVRQVVHHLADSHmNSYIRFKLSLTEETPAIRPYDEKAWSELKDSKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKEIITLENALGLYVWHSHHHIAHITELSRRmGWS 178
                                    19        29        39     |  49        59        69   |    79        89        99       109       119       129       139       149       159       169     |   
                                                              45-MSE                      73-MSE                                                                                               175-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: DinB (11)
(-)
Family: DinB_2 (5)
(-)
Bacillus subtilis (1)
1aDinB_2-1rxqD01D:30-168
1bDinB_2-1rxqD02D:30-168
1cDinB_2-1rxqD03D:30-168
1dDinB_2-1rxqD04D:30-168

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (YFIT_BACSU | O31562)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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