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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOBODY YSX1/MALTOSE BINDING PROTEIN FUSION COMPLEX
 
Authors :  R. N. Gilbreth, S. Koide
Date :  09 Apr 08  (Deposition) - 22 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Engineered Binding Protein, Antibody Mimic, Synthetic Protein Interface, Minimalist Protein Interface, De Novo Protein, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. N. Gilbreth, K. Esaki, A. Koide, S. S. Sidhu, S. Koide
A Dominant Conformational Role For Amino Acid Diversity In Minimalist Protein-Protein Interfaces
J. Mol. Biol. V. 381 407 2008
PubMed-ID: 18602117  |  Reference-DOI: 10.1016/J.JMB.2008.06.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALTOSE-BINDING PROTEIN MONOBODY YSX1 FUSION
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHFT3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MALE
    Organism Scientific: ESCHERICHIA COLI, SYNTHETIC
    Other Details: MALE INCLUDES RESIDUES 5-370, MONOBODY YSX1 377-467, 371-373 COMPRISE AN ENGINEERED LINKER
    Synonym: MBP;
MALTODEXTRIN-BINDING PROTEIN;
MMBP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric/Biological Unit (6, 18)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MN4Ligand/IonMANGANESE (II) ION
4PEG9Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:287 , GLU A:310 , ASP A:358BINDING SITE FOR RESIDUE MN A 1224
02AC2SOFTWAREASP A:236 , GLU A:359BINDING SITE FOR RESIDUE MN A 1226
03AC3SOFTWAREASP A:87 , LYS A:305 , GLY A:353 , GLN A:355BINDING SITE FOR RESIDUE EDO A 1009
04AC4SOFTWARETRP A:232 , PRO A:298 , GLY A:300 , LYS A:313 , ARG A:316 , HOH A:1054 , HOH A:1064BINDING SITE FOR RESIDUE PGE A 1011
05AC5SOFTWAREASN A:18 , ASP A:164 , ASN A:185 , ALA A:186 , LYS A:189 , LYS A:295 , ASP A:296 , HOH A:1192 , HOH A:1193BINDING SITE FOR RESIDUE PG4 A 1013
06AC6SOFTWAREASP A:65 , ARG A:66 , PRO A:331 , ILE A:333 , MET A:336 , SER A:337 , TRP A:340 , TYR A:402 , TYR A:405 , TYR A:452 , HOH A:1101 , HOH A:1121BINDING SITE FOR RESIDUE 1PE A 1014
07AC7SOFTWARETHR A:245 , PRO A:315 , ALA A:318BINDING SITE FOR RESIDUE PEG A 1001
08AC8SOFTWAREALA A:397 , TYR A:398 , SER A:400 , GLY A:427BINDING SITE FOR RESIDUE PEG A 1002
09AC9SOFTWAREGLU A:130 , ALA A:190 , PHE A:194 , PHE A:250 , LYS A:251BINDING SITE FOR RESIDUE PEG A 1003
10BC1SOFTWAREGLN A:86 , TRP A:94 , ARG A:98BINDING SITE FOR RESIDUE PEG A 1004
11BC2SOFTWAREALA A:71 , LEU A:76 , GLU A:78 , LYS A:102BINDING SITE FOR RESIDUE PEG A 1005
12BC3SOFTWARELYS A:6 , THR A:53 , GLY A:56 , ASP A:58 , ASN A:267 , ALA A:269 , ASN A:272BINDING SITE FOR RESIDUE PEG A 1006
13BC4SOFTWARETHR A:286 , GLU A:288BINDING SITE FOR RESIDUE PEG A 1007
14BC5SOFTWARETYR A:167 , PHE A:169 , LYS A:170 , TYR A:171BINDING SITE FOR RESIDUE PEG A 1008
15BC6SOFTWARELYS A:15 , ALA A:63 , GLU A:111 , LEU A:262 , LEU A:299 , HOH A:1151 , HOH A:1186BINDING SITE FOR RESIDUE PEG A 1012

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:52 -Thr A:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBP_BACTERIAL_1PS01037 Bacterial extracellular solute-binding proteins, family 1 signature.MALE_ECOLI133-150  1A:107-124

(-) Exons   (0, 0)

(no "Exon" information available for 3CSB)

(-) 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:464
 aligned with MALE_ECOLI | P0AEX9 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:464
                                                                                                                                                                                                                                                                                                                                                                                                        396                                                                                                 
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389      |  -         -         -         -         -         -         -         -         -         -    
           MALE_ECOLI    30 EGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK-------------------------------------------------------------------------------------------------   -
               SCOP domains -d3csba2 A:5-370 D-maltodextrin-binding protein, MBP                                                                                                                                                                                                                                                                                                                           ----d3csba1 A:375-467 Fibronectin, different Fn3 modules                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhh.......eeeee..hhhhhhhh........hhhhhh..hhhhhh..ee..ee..eeeeee..eeeee.........hhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh..eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhh....eeee............eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh............eeee....eeee.hhhhh...eeeeeeeeee.......eeeeee....eeee.......eeeeeeeeee...ee....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------SBP_BACTERIAL_1   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3csb A   4 TGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITKGSSGSSVPTNLEVVAATPTSLLISWDAYSSSYYVYYYRITYGETGGNSPVQEFTVPGSKSTATISGLKPGVDYTITVYAGHYLYGLLSSPISINYRT 467
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MALE_ECOLI | P0AEX9)
molecular function
    GO:1901982    maltose binding    Interacting selectively and non-covalently with maltose.
    GO:0005363    maltose transmembrane transporter activity    Enables the transfer of maltose from one side of the membrane to the other. Maltose is the disaccharide 4-O-alpha-D-glucopyranosyl-D-glucopyranose, an intermediate in the enzymatic breakdown of glycogen and starch.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0034289    detection of maltose stimulus    The series of events in which a maltose stimulus is received by a cell and converted into a molecular signal.
    GO:0042956    maltodextrin transport    The directed movement of maltodextrin, any polysaccharide of glucose residues in beta-(1,4) linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015768    maltose transport    The directed movement of maltose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Maltose is the disaccharide 4-O-alpha-D-glucopyranosyl-D-glucopyranose, an intermediate in the catabolism of glycogen and starch.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    GO:0055052    ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing    A complex for the transport of metabolites into the cell, consisting of 5 subunits: two ATP-binding subunits, two membrane spanning subunits, and one substrate-binding subunit. In organisms with two membranes, the substrate-binding protein moves freely in the periplasmic space and joins the other subunits only when bound with substrate. In organisms with only one membrane the substrate-binding protein is tethered to the cytoplasmic membrane and associated with the other subunits. Transport of the substrate across the membrane is driven by the hydrolysis of ATP.
    GO:1990060    maltose transport complex    Protein complex facilitating ATP-dependent maltose transport through inner cell membrane (periplasm to cytoplasm) in Gram-negative bacteria. In E. coli the system is composed of a periplasmic maltose-binding protein (MBP), two integral membrane proteins, MalF and MalG, and two copies of the cytoplasmic ATP-binding cassette MalK.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MALE_ECOLI | P0AEX9: 1a7l 1anf 1dmb 1ez9 1ezo 1ezp 1fqa 1fqb 1fqc 1fqd 1hsj 1iud 1jvx 1jvy 1jw4 1jw5 1lax 1lls 1mdp 1mdq 1mg1 1mh3 1mh4 1mpb 1mpc 1mpd 1n3w 1n3x 1nl5 1nmu 1omp 1peb 1r6z 1svx 1t0k 1y4c 1ytv 1ziu 1zjl 1zkb 1zmg 2d21 2h25 2klf 2mv0 2n44 2n45 2nvu 2obg 2ok2 2r6g 2v93 2vgq 2xz3 2zxt 3a3c 3c4m 3csg 3d4c 3d4g 3dm0 3ef7 3ehs 3eht 3ehu 3f5f 3g7v 3g7w 3h3g 3h4z 3hpi 3hst 3io4 3io6 3ior 3iot 3iou 3iov 3iow 3j9p 3kjt 3l2j 3lbs 3lc8 3mbp 3mp1 3mp6 3mp8 3mq9 3n94 3o3u 3oai 3osq 3osr 3pgf 3puv 3puw 3pux 3puy 3puz 3pv0 3py7 3q25 3q26 3q27 3q28 3q29 3rlf 3rum 3ser 3ses 3set 3seu 3sev 3sew 3sex 3sey 3vfj 3w15 3wai 3woa 4b3n 4bl8 4bl9 4bla 4blb 4bld 4dxb 4dxc 4edq 4egc 4exk 4fe8 4feb 4fec 4fed 4giz 4gli 4ifp 4ikm 4irl 4jbz 4jkm 4keg 4khz 4ki0 4kv3 4kyc 4kyd 4kye 4log 4mbp 4n4x 4ndz 4o2x 4ogm 4pe2 4qsz 4qvh 4r0y 4rg5 4rwf 4rwg 4tsm 4wjv 4wms 4wmt 4wmu 4wmv 4wmw 4wmx 4wrn 4wth 4wvh 4xa2 4xhs 4xr8 4xzs 4xzv 5aq9 5az6 5az7 5az8 5az9 5aza 5b3w 5b3x 5b3y 5b3z 5c7r 5cbn 5cfv 5dfm 5dis 5e24 5edu 5fio 5fsg 5gru 5gs2 5h7n 5h7q 5hz7 5hzv 5hzw 5i04 5i69 5ihj 5ii5 5iic 5iqz 5jj4 5jst 5jtq 5jtr 5ldf 5t03 5t05 5t0a 5ttd 5wpz 5wq6

(-) Related Entries Specified in the PDB File

2obg CRYSTAL STRUCTURE OF MONOBODY YS1/MALTOSE BINDING PROTEIN FUSION COMPLEX
3csg