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(-) Description

Title :  NEW STRATEGY TO ANALYZE STRUCTURES OF GLYCOPEPTIDE ANTIBIOTIC-TARGET COMPLEXES
 
Authors :  N. J. Economou, S. D. Weeks, K. C. Grasty, V. Nahoum, P. J. Loll
Date :  05 May 11  (Deposition) - 06 Jun 12  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Antibiotic, Glycopeptide, Native Protein Ligation, Fusion, Carboxymethylation Of Cysteine, Ristocetin, Sugar Binding Protein- Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. J. Economou, V. Nahoum, S. D. Weeks, K. C. Grasty, I. J. Zentner, T. M. Townsend, M. W. Bhuiya, S. Cocklin, P. J. Loll
A Carrier Protein Strategy Yields The Structure Of Dalbavancin.
J. Am. Chem. Soc. V. 134 4637 2012
PubMed-ID: 22352468  |  Reference-DOI: 10.1021/JA208755J

(-) Compounds

Molecule 1 - MALTOSE-BINDING PERIPLASMIC PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 27-392
    Gene: MALE, B4034, JW3994
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K12
    Synonym: MBP, MMBP, MALTODEXTRIN-BINDING PROTEIN
 
Molecule 2 - RISTOCETIN
    Chains: B, C
    Organism Scientific: AMYCOLATOPSIS LURIDA
    Organism Taxid: 31959

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (15, 37)

Asymmetric/Biological Unit (15, 37)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2BXY2Ligand/IonALPHA-D-ARABINOFURANOSE
3CCS1Mod. Amino AcidCARBOXYMETHYLATED CYSTEINE
4DAL2Mod. Amino AcidD-ALANINE
5GHP6OTHER(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6HTY2OTHER(BETAR)-BETA-HYDROXY-D-TYROSINE
7IPA3Ligand/IonISOPROPYL ALCOHOL
8MAL1Ligand/IonMALTOSE
9MAN4Ligand/IonALPHA-D-MANNOSE
10MDF2OTHERMETA, META'-DI-HYDROXY-PHENYLALANINE
11MP42OTHER(2S)-AMINO(3,5-DIHYDROXY-4-METHYLPHENYL)ETHANOIC ACID
12OMX2OTHER(BETAR)-BETA-HYDROXY-L-TYROSINE
13RAM2Ligand/IonALPHA-L-RHAMNOSE
14RST2Ligand/IonRISTOSAMINE
15SO44Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:16 , TRP A:63 , ALA A:64 , ASP A:66 , ARG A:67 , GLU A:112 , GLU A:154 , PRO A:155 , TYR A:156 , TRP A:341 , HOH A:549 , HOH A:550 , HOH A:614 , HOH A:627 , HOH A:703 , HOH A:813 , HOH A:826BINDING SITE FOR RESIDUE MAL A 401
02AC2SOFTWAREMET A:149 , ASN A:206 , HOH A:679 , GHP C:1 , HTY C:2BINDING SITE FOR RESIDUE IPA A 402
03AC3SOFTWAREASN A:13 , LYS A:43 , HOH A:799BINDING SITE FOR RESIDUE IPA A 403
04AC4SOFTWAREASN A:151 , GLN A:153 , GLU A:154 , ASP A:210 , TYR A:211 , HOH A:591BINDING SITE FOR RESIDUE IPA A 404
05AC5SOFTWARESER A:271 , PRO A:272 , ASN A:273 , LYS A:274 , GLU A:275 , HOH A:809 , HOH A:820 , HOH B:213BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWAREPRO A:41 , ASP A:42BINDING SITE FOR RESIDUE SO4 A 406
07AC7SOFTWARELYS A:171 , THR A:287 , ASP A:288 , GLU A:289 , HOH A:520BINDING SITE FOR RESIDUE SO4 A 407
08AC8SOFTWAREASP A:83 , LYS A:84 , MAN C:10BINDING SITE FOR RESIDUE SO4 C 107
09AC9SOFTWAREGLU A:45 , GLU A:46 , PRO A:49 , GLN A:50 , ARG A:67 , GLY A:70 , SER A:74 , THR A:81 , LYS A:128 , THR A:129 , ASP A:208 , THR A:250 , GLU A:275 , LYS A:278 , SER A:338 , TYR A:342 , ASN A:368 , ALA A:373 , GLY A:374 , CCS A:375 , LYS A:376 , DAL A:377 , DAL A:378 , HOH A:543 , HOH A:556 , HOH A:607 , HOH A:618 , HOH A:633 , HOH A:720 , HOH A:723 , HOH A:823 , HOH B:201 , HOH B:202 , HOH B:203 , HOH B:204 , HOH B:205 , HOH B:212 , HOH B:214 , HOH B:216 , HTY C:2 , MP4 C:3 , GHP C:4 , GHP C:5 , OMX C:6 , BGC C:8 , RAM C:9 , MAN C:10 , RST C:12BINDING SITE FOR CHAIN B OF RISTOCETIN
10BC1SOFTWAREGLN A:50 , LEU A:77 , ALA A:78 , GLU A:79 , THR A:81 , ASN A:101 , GLY A:102 , LYS A:103 , ILE A:105 , ASN A:206 , ASP A:208 , SER A:212 , ILE A:213 , LYS A:220 , ALA A:269 , LYS A:274 , IPA A:402 , HOH A:516 , HOH A:560 , HOH A:651 , HOH A:686 , HOH A:704 , HOH A:723 , HOH A:731 , HOH A:749 , HTY B:2 , MP4 B:3 , GHP B:4 , GHP B:5 , OMX B:6 , BGC B:8 , MAN B:10 , BXY B:11 , RST B:12 , SO4 C:107 , HOH C:201 , HOH C:202 , HOH C:204 , HOH C:205 , HOH C:207 , HOH C:208 , HOH C:209 , HOH C:211 , HOH C:217 , HOH C:219 , HOH C:221BINDING SITE FOR CHAIN C OF RISTOCETIN

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ghp B:5 -Omx B:6
2Ghp C:5 -Omx C:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:108-125

(-) Exons   (0, 0)

(no "Exon" information available for 3RUM)

(-) 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:378
 aligned with MALE_ECOLI | P0AEX9 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:378
                                                                                                                                                                                                                                                                                                                                                                                                            396        
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395|       
           MALE_ECOLI    26 AKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK-------   -
               SCOP domains d3ruma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.....hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh......eeeee..hhhhhhhh........hhhhhh..hhhhhhhhee..ee..eeeeee..eeeee.........hhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh..eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhhh..eeee...ee..ee...eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------SBP_BACTERIAL_1   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rum A   1 MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAAAAAGcKxx 378
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    | ||
                                                                                                                                                                                                                                                                                                                                                                                                                375-CCS
                                                                                                                                                                                                                                                                                                                                                                                                                  377-DAL
                                                                                                                                                                                                                                                                                                                                                                                                                   378-DAL


Chain B from PDB  Type:OTHER  Length:7
                                       
                 3rum B   1 xxxxxxx   7
                            |||||||
                            |||||||
                            1-GHP||
                             2-HTY|
                              3-MP4
                               4-GHP
                                5-GHP
                                 6-OMX
                                  7-MDF


Chain C from PDB  Type:OTHER  Length:7
                                       
                 3rum C   1 xxxxxxx   7
                            |||||||
                            |||||||
                            1-GHP||
                             2-HTY|
                              3-MP4
                               4-GHP
                                5-GHP
                                 6-OMX
                                  7-MDF
   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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 3csb 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 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

1anf MALTODEXTRIN BINDING PROTEIN WITH BOUND MALTOSE
3rul
3run
3vfj
3vfk