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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOHEPTOSE ISOMERASE (BH3325) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 Apr 08  (Deposition) - 06 May 08  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rossmann Fold, 3-Layer (Aba) Sandwich, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Phosphoheptose Isomerase (Np_244191. 1) From Bacillus Halodurans At 2. 00 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PHOSPHOHEPTOSE ISOMERASE
    Atcc: BAA-125
    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: NP_244191.1, BH3325
    Organism Scientific: BACILLUS HALODURANS C-125
    Organism Taxid: 272558
    Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153
    Synonym: UPF0309 PROTEIN BH3325

 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, 43)

Asymmetric Unit (4, 43)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MG2Ligand/IonMAGNESIUM ION
4MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
4MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 21)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
4MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:53 , GLU A:57 , HIS B:53 , GLU B:57BINDING SITE FOR RESIDUE MG A 243
02AC2SOFTWAREHIS C:53 , GLU C:57 , HIS D:53 , GLU D:57BINDING SITE FOR RESIDUE MG C 243
03AC3SOFTWAREPRO A:74 , TYR A:99 , HIS A:103 , ARG C:82 , LYS C:85BINDING SITE FOR RESIDUE ACT A 244
04AC4SOFTWAREPRO B:74 , TYR B:99 , HIS B:103 , ARG D:82 , LYS D:85BINDING SITE FOR RESIDUE ACT B 243
05AC5SOFTWAREARG A:82 , LYS A:85 , PRO C:74 , TYR C:99 , HIS C:103BINDING SITE FOR RESIDUE ACT C 244
06AC6SOFTWARELYS B:85 , PRO D:74 , TYR D:99 , HIS D:103BINDING SITE FOR RESIDUE ACT D 243
07AC7SOFTWARESER D:49 , GLU D:90 , SER D:115 , ASN D:116 , SER D:117BINDING SITE FOR RESIDUE EDO D 244
08AC8SOFTWAREASN C:13 , SER C:17 , ASN D:13 , SER D:17BINDING SITE FOR RESIDUE EDO D 245
09AC9SOFTWAREASN A:13 , SER A:17 , ASN B:13 , SER B:17BINDING SITE FOR RESIDUE EDO A 245
10BC1SOFTWARELEU C:79 , PRO C:83 , ASN C:84 , SER C:86 , ASN D:61BINDING SITE FOR RESIDUE EDO C 245
11BC2SOFTWAREGLY B:94 , LYS B:97 , SER B:98 , LYS B:101BINDING SITE FOR RESIDUE EDO B 244

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.Y3325_BACHD34-217
 
 
 		  4A:34-217
B:34-217
C:34-217
D:34-217
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.Y3325_BACHD34-217
 
 
 		  2A:34-217
B:34-217
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.Y3325_BACHD34-217
 
 
 		  2-
-
C:34-217
D:34-217

(-) Exons   (0, 0)

(no "Exon" information available for 3CVJ)

(-) 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:243
 aligned with Y3325_BACHD | Q9K7N6 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:243
                             1                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239   
          Y3325_BACHD     - -MTSSFTDYCKFFNRILSEVQETQEQAIIKGAHLVSEAVMNGGRFYVFGSGHSHMIAEEIYNRAGGLALVTAILPPELMLHERPNKSTYLERIEGLSKSYLKLHQVTNKDVIMIISNSGRNTVPVEMAIESRNIGAKVIAMTSMKHSQKVTSRHKSGKKLYEYADVVLDNGAPVGDAGFQIANSEIYSGATSDSIGCFLAQALIVETLHLLVQQGFEPPVFKSSNVDGADLYNDKIFNEYVKW 242
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cvjA00 A:0-242 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhh.........eee..hhhhh.....hhhhhhh...hhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhh.eeeeeehhhhhhhh........hhhhhh.eeee.........ee......ee..hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------SIS  PDB: A:34-217 UniProt: 34-217                                                                                                                                                      ------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvj A   0 GmTSSFTDYCKFFNRILSEVQETQEQAIIKGAHLVSEAVmNGGRFYVFGSGHSHmIAEEIYNRAGGLALVTAILPPELmLHERPNKSTYLERIEGLSKSYLKLHQVTNKDVImIISNSGRNTVPVEmAIESRNIGAKVIAmTSmKHSQKVTSRHKSGKKLYEYADVVLDNGAPVGDAGFQIANSEIYSGATSDSIGCFLAQALIVETLHLLVQQGFEPPVFKSSNVDGADLYNDKIFNEYVKW 242
                             |       9        19        29        39        49    |   59        69        79        89        99       109  |    119      |129       139|  |   149       159       169       179       189       199       209       219       229       239   
                             |                                    39-MSE         54-MSE                  78-MSE                           112-MSE       126-MSE       140-MSE                                                                                                  
                             1-MSE                                                                                                                                       143-MSE                                                                                               


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with Y3325_BACHD | Q9K7N6 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:243
                             1                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239   
          Y3325_BACHD     - -MTSSFTDYCKFFNRILSEVQETQEQAIIKGAHLVSEAVMNGGRFYVFGSGHSHMIAEEIYNRAGGLALVTAILPPELMLHERPNKSTYLERIEGLSKSYLKLHQVTNKDVIMIISNSGRNTVPVEMAIESRNIGAKVIAMTSMKHSQKVTSRHKSGKKLYEYADVVLDNGAPVGDAGFQIANSEIYSGATSDSIGCFLAQALIVETLHLLVQQGFEPPVFKSSNVDGADLYNDKIFNEYVKW 242
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cvjB00 B:0-242 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhh.........eeee.hhhhh.....hhhhhhh...hhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhh.eeeeeehhhhhhhh........hhhhhh.eeee.........ee......ee..hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------SIS  PDB: B:34-217 UniProt: 34-217                                                                                                                                                      ------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvj B   0 GmTSSFTDYCKFFNRILSEVQETQEQAIIKGAHLVSEAVmNGGRFYVFGSGHSHmIAEEIYNRAGGLALVTAILPPELmLHERPNKSTYLERIEGLSKSYLKLHQVTNKDVImIISNSGRNTVPVEmAIESRNIGAKVIAmTSmKHSQKVTSRHKSGKKLYEYADVVLDNGAPVGDAGFQIANSEIYSGATSDSIGCFLAQALIVETLHLLVQQGFEPPVFKSSNVDGADLYNDKIFNEYVKW 242
                             |       9        19        29        39        49    |   59        69        79        89        99       109  |    119      |129       139|  |   149       159       169       179       189       199       209       219       229       239   
                             1-MSE                                39-MSE         54-MSE                  78-MSE                           112-MSE       126-MSE       140-MSE                                                                                                  
                                                                                                                                                                         143-MSE                                                                                               


Chain C from PDB  Type:PROTEIN  Length:242
 aligned with Y3325_BACHD | Q9K7N6 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
          Y3325_BACHD     1 MTSSFTDYCKFFNRILSEVQETQEQAIIKGAHLVSEAVMNGGRFYVFGSGHSHMIAEEIYNRAGGLALVTAILPPELMLHERPNKSTYLERIEGLSKSYLKLHQVTNKDVIMIISNSGRNTVPVEMAIESRNIGAKVIAMTSMKHSQKVTSRHKSGKKLYEYADVVLDNGAPVGDAGFQIANSEIYSGATSDSIGCFLAQALIVETLHLLVQQGFEPPVFKSSNVDGADLYNDKIFNEYVKW 242
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3cvjC00 C:2-242 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhh.........eeee.hhhhh.....hhhhhhh...hhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhh.eeeeeehhhhhhhh........hhhhhh.eeee.........ee......ee..hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------SIS  PDB: C:34-217 UniProt: 34-217                                                                                                                                                      ------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvj C   1 mTSSFTDYCKFFNRILSEVQETQEQAIIKGAHLVSEAVmNGGRFYVFGSGHSHmIAEEIYNRAGGLALVTAILPPELmLHERPNKSTYLERIEGLSKSYLKLHQVTNKDVImIISNSGRNTVPVEmAIESRNIGAKVIAmTSmKHSQKVTSRHKSGKKLYEYADVVLDNGAPVGDAGFQIANSEIYSGATSDSIGCFLAQALIVETLHLLVQQGFEPPVFKSSNVDGADLYNDKIFNEYVKW 242
                            |       10        20        30        40        50   |    60        70       |80        90       100       110 |     120     | 130       140  |    150       160       170       180       190       200       210       220       230       240  
                            1-MSE                                39-MSE         54-MSE                  78-MSE                           112-MSE       126-MSE       140-MSE                                                                                                  
                                                                                                                                                                        143-MSE                                                                                               


Chain D from PDB  Type:PROTEIN  Length:242
 aligned with Y3325_BACHD | Q9K7N6 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
          Y3325_BACHD     1 MTSSFTDYCKFFNRILSEVQETQEQAIIKGAHLVSEAVMNGGRFYVFGSGHSHMIAEEIYNRAGGLALVTAILPPELMLHERPNKSTYLERIEGLSKSYLKLHQVTNKDVIMIISNSGRNTVPVEMAIESRNIGAKVIAMTSMKHSQKVTSRHKSGKKLYEYADVVLDNGAPVGDAGFQIANSEIYSGATSDSIGCFLAQALIVETLHLLVQQGFEPPVFKSSNVDGADLYNDKIFNEYVKW 242
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3cvjD00 D:2-242 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhh.........eee..hhhhh.....hhhhhhh...hhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhh.eeeeeehhhhhhhh........hhhhhh.eeee.........ee......ee..hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------SIS  PDB: D:34-217 UniProt: 34-217                                                                                                                                                      ------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvj D   1 mTSSFTDYCKFFNRILSEVQETQEQAIIKGAHLVSEAVmNGGRFYVFGSGHSHmIAEEIYNRAGGLALVTAILPPELmLHERPNKSTYLERIEGLSKSYLKLHQVTNKDVImIISNSGRNTVPVEmAIESRNIGAKVIAmTSmKHSQKVTSRHKSGKKLYEYADVVLDNGAPVGDAGFQIANSEIYSGATSDSIGCFLAQALIVETLHLLVQQGFEPPVFKSSNVDGADLYNDKIFNEYVKW 242
                            |       10        20        30        40        50   |    60        70       |80        90       100       110 |     120     | 130       140  |    150       160       170       180       190       200       210       220       230       240  
                            1-MSE                                39-MSE         54-MSE                  78-MSE                           112-MSE       126-MSE       140-MSE                                                                                                  
                                                                                                                                                                        143-MSE
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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 3CVJ)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Y3325_BACHD | Q9K7N6)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    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.

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